ENCODE Project at NHGRI ENCODE Project at UCSC

10 Latest Changes (all assemblies)
 
Track/Table Name Assembly Release Date
GENCODE V20 / Ensembl 76 release for GRCh38 hg38 13 Oct 2014
Genome State Segmentations from ENCODE hg19 17 Apr 2014
GENCODE Gene annotations for mouse, Version M2 mm10 11 Mar 2014
Initial hg38 release (using GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2)): Assembly, Hg19 Diff, Alt Map, Gap, GC Percent, GRC Contigs, INSDC, Scaffolds, RefSeq Genes, GENCODE Genes V19, Genscan Genes, MGC Genes, ORFeome Clones, Other RefSeq, Human mRNAs, Spliced ESTs, Human ESTs, Other ESTs, Other mRNAs, CpG Islands, Dog Chain/Net, Mouse Chain/Net, Primate Chain/Net, Self Chain, RepeatMasker, Interrupted Repeats, Simple Repeats, WM + SDust hg38 06 Mar 2014
ENCODE Regulation: Txn Factor ChIP Clusters (update to 161 TF targets, from uniform processing of June 2012 freeze) hg19 24 Jan 2014
GENCODE V19 release hg19 15 Jan 2014
GENCODE Version 17 release hg19 05 Aug 2013
Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis hg19 10 May 2013
ENCODE Regulation: DNase Clusters (update to 125 cell types using ENCODE uniform peaks from Jan 2011 freeze) hg19 25 Jan 2013
DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis hg19 22 Jan 2013

Human Dec. 2013 (GRCh38/hg38) (hg38, GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2))
 
Track/Table Name Release Date
GENCODE V20 / Ensembl 76 release for GRCh38 13 Oct 2014
Initial hg38 release (using GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2)): Assembly, Hg19 Diff, Alt Map, Gap, GC Percent, GRC Contigs, INSDC, Scaffolds, RefSeq Genes, GENCODE Genes V19, Genscan Genes, MGC Genes, ORFeome Clones, Other RefSeq, Human mRNAs, Spliced ESTs, Human ESTs, Other ESTs, Other mRNAs, CpG Islands, Dog Chain/Net, Mouse Chain/Net, Primate Chain/Net, Self Chain, RepeatMasker, Interrupted Repeats, Simple Repeats, WM + SDust 06 Mar 2014

Human Feb. 2009 (GRCh37/hg19) (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))
 
Track/Table Name Release Date
Genome State Segmentations from ENCODE 17 Apr 2014
ENCODE Regulation: Txn Factor ChIP Clusters (update to 161 TF targets, from uniform processing of June 2012 freeze) 24 Jan 2014
GENCODE V19 release 15 Jan 2014
GENCODE Version 17 release 05 Aug 2013
Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis 10 May 2013
ENCODE Regulation: DNase Clusters (update to 125 cell types using ENCODE uniform peaks from Jan 2011 freeze) 25 Jan 2013
DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis 22 Jan 2013
GENCODE Version 14 release 17 Jan 2013
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) 26 Sep 2012
Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill) (Release 2) 19 Sep 2012
Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. 11 Sep 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (Release 3) 10 Sep 2012
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) (Release 3) 28 Aug 2012
Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) (Release 2) 27 Aug 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 3) 20 Aug 2012
RNA Sub-cellular Localization by Paired-end diTag Sequencing from ENCODE/GIS (Release 2) 14 Aug 2012
RNA-seq from ENCODE/Caltech (Release 4) 08 Aug 2012
Histone Modifications by ChIP-seq from ENCODE/Broad Institute (Release 3) 06 Aug 2012
DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 4) 06 Aug 2012
Affymetrix Exon Array from ENCODE/University of Washington (Release 4) 31 Jul 2012
Replication Timing by Repli-chip from ENCODE/FSU (Release 2) 31 Jul 2012
DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha (Release 3) 30 Jul 2012
RNA Subcellular CAGE Localization from ENCODE/RIKEN (Release 4) 30 Jul 2012
Histone Modifications by ChIP-seq from ENCODE/University of Washington (Release 5) 24 Jul 2012
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 6) 23 Jul 2012
Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. (Release 2) 18 Jul 2012
Affymetrix Exon Array from ENCODE/University of Washington (Release 3) 12 Jul 2012
Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE 10 Jul 2012
Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) 09 Jul 2012
Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. (Release 2) 09 Jul 2012
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2) 21 Jun 2012
Gene Annotations from ENCODE/GENCODE Version 12 21 Jun 2012
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 3) 15 Jun 2012
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 5) 12 Jun 2012
Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan 24 May 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard (Release 2) 14 May 2012
RNA Subcellular CAGE Localization from ENCODE/RIKEN (Release 3) 02 May 2012
RNA-seq from ENCODE/Caltech (Release 3) 19 Apr 2012
Replication Timing by Repli-chip from ENCODE/FSU 18 Apr 2012
Histone Modifications by ChIP-seq from ENCODE/University of Washington (Release 4) 11 Apr 2012
Affymetrix Exon Array from ENCODE/Duke (Release 3) 04 Apr 2012
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University) (Release 2) 28 Mar 2012
ENCODE Pilot (regions lifted from hg18) 26 Mar 2012
Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. 22 Mar 2012
Gene Annotations from ENCODE/GENCODE Version 11 08 Mar 2012
Histone Modifications by ChIP-seq from ENCODE/Broad Institute (Release 2) 06 Mar 2012
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 4) 06 Mar 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB (Release 2) 29 Feb 2012
CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington (Release 3) 29 Feb 2012
RNA-seq from ENCODE/HAIB 23 Feb 2012
Gene Annotations from ENCODE/GENCODE Version 10 22 Feb 2012
Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2) 22 Feb 2012
Histone Modifications by ChIP-seq from ENCODE/University of Washington (Release 3) 16 Feb 2012
Replication Timing by Repli-seq from ENCODE/University of Washington 14 Feb 2012
DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 3) 13 Feb 2012
DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) (Release 2) 10 Feb 2012
Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha (Release 2) 20 Jan 2012
RNA-seq from ENCODE/Caltech (Release 2) 17 Jan 2012
CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington (Release 2) 17 Jan 2012
Affymetrix Exon Array from ENCODE/University of Washington (Release 2) 04 Jan 2012
RNA Subcellular CAGE Localization from ENCODE/RIKEN 22 Dec 2011
CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB 01 Dec 2011
Histone Modifications by ChIP-seq from ENCODE/University of Washington 17 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard 29 Oct 2011
ENCODE Mapability (hg19 release 3) 28 Oct 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 3) 19 Oct 2011
RNA Subcellular Localization by Paired End diTag Sequencing from GIS/ENCODE 17 Oct 2011
Long RNA-seq from ENCODE/Cold Spring Harbor Lab 17 Oct 2011
Affymetrix Exon Array from ENCODE/Duke (Release 2) 13 Oct 2011
Chromatin Interactions by 5C from ENCODE/University of Washington 10 Oct 2011
Histone Modifications by ChIP-seq from ENCODE/SYDH (Release 2) 07 Oct 2011
RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany (Release 2 - fixed p & q values and scores) 04 Oct 2011
DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha (Release 2) 30 Sep 2011
Proteogenomics from ENCODE/Univ. North Carolina/Boise State Univ. 29 Sep 2011
RNA-seq from ENCODE/Stanford/Yale/USC/Harvard 08 Sep 2011
RIP-seq from ENCODE/SUNY Albany 29 Aug 2011
Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha 16 Aug 2011
RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany 15 Aug 2011
Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU 29 Jul 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB 18 Jul 2011
Gene Annotations from ENCODE/GENCODE Version 7 11 Jul 2011
Chromatin State Segmentation by HMM from ENCODE/Broad 24 Jun 2011
Affymetrix Exon Array from ENCODE/Duke 14 Jun 2011
DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA) 10 Jun 2011
Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago 03 Jun 2011
Integrated Regulation from ENCODE Tracks (Transcription, Layered H3K4Me1, Layered H3K4Me3, Layered H3K27Ac, DNase Clusters, Txn Factor ChIP) 19 May 2011
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard 19 May 2011
ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius Lab) 18 May 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington 04 May 2011
RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany 28 Apr 2011
Open Chromatin by DNaseI HS from ENCODE/Duke University 19 Apr 2011
DNaseI Digital Genomic Footprinting from ENCODE/University of Washington (Release 2) 07 Apr 2011
Affymetrix Exon Array from ENCODE/University of Washington 01 Apr 2011
RNA CAGE Subcellular Localization from ENCODE/RIKEN 23 Mar 2011
Open Chromatin by FAIRE-seq from ENCODE/UNC 21 Mar 2011
CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington 17 Mar 2011
Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) 17 Mar 2011
RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany 14 Feb 2011
Histone Modifications by ChIP-seq from ENCODE/University of Washington 11 Feb 2011
Histone Modifications by ChIP-seq from ENCODE/Broad Institute 10 Feb 2011
ENCODE Caltech (Wold Lab) RNA-seq 08 Feb 2011
ENCODE GIS DNA PET (update: added fastq files) 12 Jan 2011
ENCODE UW DNaseI HS 16 Dec 2010
ENCODE HAIB Methyl RRBS 15 Dec 2010
ENCODE UW DNaseI DGF 14 Dec 2010
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array 03 Dec 2010
ENCODE CSHL Sm RNA-seq 17 Nov 2010
ENCODE Genome Institute of Singapore RNA-seq 17 Nov 2010
ENCODE Gencode Gene Annotations (V4) 15 Sep 2010
ENCODE Genome Institute of Singapore DNA Paired-End Ditags 08 Sep 2010
ENCODE Mapability or Uniqueness of Reference Genome 03 Jun 2010

Human Mar. 2006 (NCBI36/hg18) (hg18, NCBI Build 36.1)
 
Track/Table Name Release Date
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI - Validation data (Release 5) 11 Oct 2011
ENCODE Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH 24 Jun 2011
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard 03 Jun 2011
ENCODE Common Cell CNV (Release 2): colors in Regions view subtracks updated to new standards 08 Apr 2011
ENCODE UW DNaseI HS (Release 4): Jurkat (G1 Phase) and HIPEpic replicates have been revoked 24 Feb 2011
ENCODE Regulation 12 Aug 2010
ENCODE HudsonAlpha RNA-seq 30 Jul 2010
ENCODE RNA-seq from Yale/UC-Davis/Harvard 09 Jul 2010
ENCODE Boston Univ (Tullius Lab) ORChID Predicted DNA Cleavage Sites 29 Jun 2010
ENCODE Broad Histone (update to Release 3) - improved display of Signal subtracks when zoomed in to a range spanning less than 16,500 base pairs. 16 Jun 2010
ENCODE HAIB TFBS (release 2) 11 Jun 2010
ENCODE Caltech RNA-seq (Release 2) 10 Jun 2010
ENCODE Mapability or Uniqueness of Reference Genome (update: adding CRG Alignability data) 03 Jun 2010
ENCODE GIS Subcellular RNA Localization by Paired End diTag Sequencing 01 Jun 2010
ENCODE Genome Institute of Singapore RNA-seq 26 May 2010
ENCODE Yale TFBS (release 3) 26 May 2010
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags (Release 2) 24 May 2010
ENCODE Duke Affy All-Exon Arrays 24 May 2010
ENCODE Univ. Washington Digital DNase Genomic Footprinting 17 May 2010
ENCODE Genome Institute of Singapore DNA Paired-End Ditags 19 Apr 2010
Fixed corrupt table from ENCODE pilot project: Gencode Gene Annotations (March 2007) 09 Apr 2010
ENCODE Open Chromatin (release 3) 31 Mar 2010
ENCODE Histone Modifications by Broad Institute ChIP-seq (release 3) 23 Mar 2010
ENCODE UW Affy All-Exon Arrays (release 2) 18 Mar 2010
ENCODE Histone Modifications by Univ. Washington ChIP-seq 11 Mar 2010
ENCODE HudsonAlpha Methyl-seq 05 Mar 2010
ENCODE Gencode Gene Annotations (Version 3c) 26 Feb 2010
ENCODE Cold Spring Harbor Labs Small RNA-seq 26 Feb 2010
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI (Release 2) 03 Feb 2010
ENCODE Broad Histone Release 2 (release 2) 18 Dec 2009
ENCODE Caltech RNA-seq Map Algorithm 18 Dec 2009
ENCODE Cold Spring Harbor Labs Long RNA-seq (Release 2: GM12878, K562 whole cell) 17 Dec 2009
ENCODE Open Chromatin, Duke/UNC/UT (Release 2) 04 Dec 2009
ENCODE RIKEN CAGE Loc: updated download files 30 Nov 2009
ENCODE Yale TFBS (Update several subtracks; add new subtracks) 14 Oct 2009
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array (Update: GM12878 Nucleolus Total, HepG2 Nucleus PolyA+ and PolyA-, HepG2 Nucleolus Total) 02 Oct 2009
ENCODE NHGRI Elnitski Negative Regulatory Elements 24 Sep 2009
ENCODE UW Affy All Exon Arrays 15 Sep 2009
ENCODE Common Cell-Type Copy Number Variation 11 Sep 2009
ENCODE HudsonAlpha Methyl-seq 11 Sep 2009
ENCODE HudsonAlpha CpG Methylation by Illumina Methyl27 11 Sep 2009
ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI 11 Sep 2009
ENCODE HudsonAlpha CHIP-seq (Correction to labels and metadata - TAF1) 13 Aug 2009
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags: PolyA- in K562 nucleus and cytosol, PolyA- in prostate whole cell 13 Aug 2009
ENCODE Cold Spring Harbor Labs Long RNA-seq (K562) 11 Aug 2009
ENCODE Helicos RNA-seq (K562) 28 Jul 2009
ENCODE Mapability or Uniqueness of Reference Genome 24 Jul 2009
ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array 06 Jul 2009
ENCODE Open Chromatin, Duke/UNC/UT 26 Jun 2009
ENCODE RIKEN RNA Subcellular Localization by CAGE Tags 09 Jun 2009
ENCODE HudsonAlpha Transcription Factor Binding Sites by ChIP-seq 05 Jun 2009
ENCODE Gencode Gene Annotations 08 May 2009
ENCODE SUNY Albany RNA Binding Proteins by RIP-chip 08 Apr 2009
ENCODE Histone Modifications by Broad Institute ChIP-seq (Raw Signal tracks) 03 Apr 2009
ENCODE Histone Modifications by Broad Institute ChIP-seq 03 Apr 2009
ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard 13 Mar 2009
ENCODE cell culture protocols 09 Mar 2009
ENCODE portal update for production phase 23 Jan 2009
ENCODE 36-Way TBA Alignments and Conservation 19 Dec 2008
Affymetrix ENCODE Extension Transcription Sites & Signal 16 Apr 2008
ENCODE NHGRI DIPs (lift from hg17) 23 Oct 2007
Whole-Genome ENCODE LI/UCSD TAF1 Super Track 17 Oct 2007
ENCODE data migration from hg17 08 Oct 2007

Human May 2004 (NCBI35/hg17) (hg17, NCBI Build 35)
 
Track/Table Name Release Date
ENCODE TBA SCONE Conservation (Update) 19 Oct 2007
ENCODE UC Davis ChIP-chip NimbleGen (E2F1, c-Myc, TAF, POLII) 24 Jul 2007
ENCODE Yale ChIP-chip Sites - Jun07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Jun07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Jun07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sites - Apr07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Apr07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Apr07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sites - Update to Jan07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Jan07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Pval - Jan07 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sites Update to Nov06 batch 13 Jul 2007
ENCODE Yale ChIP-chip Sig - Nov06 batch 13 Jul 2007
ENCODE University of Virginia DNA Replication Origins (data update) 30 May 2007
ENCODE Duke Dnase/chip - Feb07 batch (data addition) 21 May 2007
ENCODE Gencode RACEfrags 18 May 2007
ENCODE Gencode Gene Annotations (March 2007) 04 May 2007
ENCODE UCD Ng ChIP Hits (update of cMyc and E2F1 data) 17 Apr 2007
ENCODE Yale RFBR (Regulatory Factor Binding Regions) 21 Feb 2007
ENCODE: UCSC EvoFold (Encode predictions analyzed in Washietl, Pedersen, et al., 2007). Replaces TBA23 EvoFold data. 13 Feb 2007
ENCODE - University of Vienna, RNA secondary structure predicted by RNAz 16 Jan 2007
ENCODE Yale RNA (update with October 2005 freeze data) 10 Jan 2007
ENCODE UW/Reg QCP DNaseI Sens (replaces the following three tracks: UW/Reg DNaseI HSs, UW/Reg Q/A, UW DNase GM) 07 Dec 2006
ENCODE Duke/NHGRI DNase (New Chip method in HepG2, Hela, GM, and CD4+) 05 Dec 2006
ENCODE UT-Austin STAGE (update to add STAT1 tags) 29 Nov 2006
ENCODE GIS Chip-PET (P53 in HCT116, STAT1 in HeLa, c-Myc in P493) 07 Nov 2006
ENCODE NHGRI/PSU/UCSC TBA Conserved Elements 05 Oct 2006
ENCODE NHGRI/PSU/UCSC TBA Conservation 05 Oct 2006
ENCODE NHGRI/PSU TBA Alignments 05 Oct 2006
ENCODE MSA Consensus Constrained Elements 04 Oct 2006
ENCODE UC Berkeley MAVID Alignments 04 Oct 2006
ENCODE UC Berkeley MAVID Conservation 04 Oct 2006
ENCODE UC Berkeley MAVID Conserved Elements 04 Oct 2006
ENCODE Stanford MLAGAN Conserved Elements 04 Oct 2006
ENCODE Stanford MLAGAN Conservation 04 Oct 2006
ENCODE Stanford MLAGAN Alignments 04 Oct 2006
ENCODE MSA Alignment Gaps 04 Oct 2006
ENCODE MSA Alignment Agreement 04 Oct 2006
ENCODE UNC FAIRE track (data update) 21 Aug 2006
8 new subtracks for ENCODE Sanger ChIP-chip track 17 Aug 2006
ENCODE University of Uppsala, Sweden ChIP-chip Na-butyrate time series 26 Jun 2006
ENCODE UNC FAIRE Peaks (ChIPOTle) Apr. 2006 Update, new subtrack added to UNC FAIRE 15 Jun 2006
ENCODE UW DNase/Array GM06990 13 Jun 2006
ENCODE Sanger ChIP (additional data in HFL-1 cell line) 24 May 2006
ENCODE Detection of LinEage Specific Selection (DLESS) 19 May 2006
ENCODE Yale ChIP Sites (data replaced with 5 new transcription factors). Previous track Yale ChIP Sites renamed Yale STAT1 Sites. 13 Jan 2006
ENCODE Yale ChIP Signal (data replaced with 5 new transcription factors). Previous track Yale ChIP Signal renamed Yale STAT1 Signal. 13 Jan 2006
ENCODE Yale ChIP pVal (data replaced with 5 new transcription factors). Previous track Yale ChIP pVal renamed Yale STAT1 pVal. 13 Jan 2006
ENCODE EGASP Partial (data correction) 11 Jan 2006
Recomb Hotspots: ENCODE recombination hotspots and rates 06 Jan 2006
ENCODE Uppsala Chip (University of Uppsala, Sweden ChIP-chip coordinate corrections) 03 Jan 2006
ENCODE Yale TAR (Replace June data with new methods) 02 Jan 2006
ENCODE UVa DNA Rep Ori (University of Virginia DNA Replication Origins, Oct 2005 Freeze) 29 Dec 2005
ENCODE UT-Austin STAGE (Sequence Tag Analysis of Genomic Enrichment), c-Myc in HeLa cells 28 Dec 2005
ENCODE Affy Transfrags (updated HeLa data) 21 Dec 2005
ENCODE Affy RNA Signal (updated HeLa data) 21 Dec 2005
ENCODE UVa DNA Rep TR50 (University of Virginia DNA Smoothed Timing at 50% Replication, Oct 2005 Freeze) 16 Dec 2005
ENCODE UVa DNA Rep Seg (University of Virginia DNA Replication Temporal Segmentation, Oct 2005 Freeze) 02 Dec 2005
ENCODE Sanger ChIP Hits (Peaks and Centers, Oct 2005 Freeze) 22 Nov 2005
ENCODE Sanger ChIP (H3, H4 histones in GM, K562 and HeLa cells, Oct 2005 Freeze) 22 Nov 2005
ENCODE UNC FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements, Oct 2005 Freeze) 22 Nov 2005
ENCODE UCD Ng ChIP (UC Davis ChIP-chip of E2F1, Myc in HeLa, Oct 2005 Freeze) 18 Nov 2005
ENCODE Uppsala Chip (University of Uppsala, Sweden ChIP-chip of H3ac,HNF3b,HNF4a,USF1 in HepG2 cells, Oct 2005 Freeze) 18 Nov 2005
ENCODE Affy Strict Sites (Affymetrix ChIP-chip of 5 factors in HL60 cells, Oct 2005 Freeze) 18 Nov 2005
ENCODE Affy Strict (Affymetrix ChIP-chip of 5 factors in HL60 cells, Oct 2005 Freeze) 18 Nov 2005
ENCODE Affy Strict Pval (Affymetrix ChIP-chip on 5 factors, in HL60 cells, Oct 2005 Freeze) 18 Nov 2005
ENCODE Affy RNA (RNA abundance and transfrags, Oct 2005 Freeze) 07 Nov 2005
ENCODE UT-Austin ChIP (c-Myc and EF24 in HeLa and 20901 fibroblasts, Oct 2005 Freeze) 07 Nov 2005
ENCODE NHGRI DnaseI-HS (MPSS and Chip methods, in CD4 and GM09660, Oct 2005 Freeze) 07 Nov 2005
ENCODE GIS PET RNA (update Oct 2005 Freeze and new estrogen-treated MCF7) 07 Nov 2005
ENCODE Gencode Genes (Oct 2005 Freeze) 07 Nov 2005
ENCODE LI Ng gIF ChIP (Addition of 5 antibodies, in HeLa cells) 27 Oct 2005
ENCODE EGASP Update (Add Fgenesh++ corrected predictions) 14 Oct 2005
ENCODE GIS STAT1 +/- gIF HeLa 14 Oct 2005
ENCODE UVa DNA Rep Seg, UVa DNA Rep Ori (DNA replication timing segmentation and origins) 04 Oct 2005
ENCODE YALE MAS TAR (additional data) 27 Sep 2005
ENCODE YALE MAS RNA (additional data from June freeze) 27 Sep 2005
ENCODE BU Orchid 21 Sep 2005
ENCODE NHGRI DIPs: Whole Genome Shotgun insertion/deletion polymorphisms from Jim Mullikin/SSAHA 21 Sep 2005
ENCODE: LI Ng gIF ChIP (HeLa) 20 Sep 2005
ENCODE: LI Ng Validation (Pol2, Taf1, H3K4me, H3ac) 20 Sep 2005
ENCODE Sanger ChIP-chip 20 Sep 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - Pol II, TAF1, AcH3, H3K4me, SUZ12, and H3K27me antibodies - repackage three existing tracks into one 20 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, P-Values) 20 Sep 2005
ENCODE: LI gIF ChIP (HeLa) 19 Sep 2005
ENCODE HapMap Allele Frequencies 19 Sep 2005
ENCODE: GIS P53 5FU HCT116 19 Sep 2005
ENENCODE: Affy Transfrags, Affy pVal {0,2,8,32}h, Affy Sites {0,2,8,32}h 16 Sep 2005
ENCODE: Affy RNA Signal 16 Sep 2005
ENCODE: Yale MAS array, RNA Transcript Map, Placenta, Nimblegen Protocol 16 Sep 2005
ENCODE: Yale MAS array, RNA Transcriptionally Active Regions, Placenta, Nimblegen Protocol 16 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Signal) 16 Sep 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Binding Sites) 16 Sep 2005
ENCODE: Yale TAR 16 Sep 2005
ENCODE: Stanford Endogenous Transcript Levels in HCT116 Cells; Stanford ChIP-chip (HCT116, Jurkat, K562 cells; Sp1, Sp3 ChIP); Stanford ChIP-chip Smoothed Score; Stanford Methylation Digest: Be2C, CRL1690, HCT116, HT1080, HepG2, JEG3, Snu182, U87; Stanford Methylation Digest Smoothed Score 16 Sep 2005
ENCODE: Stanf Promoter 15 Sep 2005
ENCODE: BU First Exon 15 Sep 2005
ENCODE: Yale RNA 15 Sep 2005
ENCODE: Sanger Assoc 15 Sep 2005
ENCODE: UC Davis ChIP-chip Nimblegen - E2F1 ab, HeLa Cells 15 Sep 2005
ENCODE: GIS RNA PET 15 Sep 2005
ENCODE: TBA23 EvoFold (Predictions of RNA Secondary Structure Using TBA23, ENCODE Regions only) 15 Sep 2005
ENCODE: Known+Pred RNA (Known and Predicted RNA Transcription) 15 Sep 2005
ENCODE: UW/Regulome DNase I Hypersensitivity Probability 14 Sep 2005
ENCODE: Regulome DNase I Hypersensitivity 14 Sep 2005
ENCODE: NHGRI DNaseI-HS 14 Sep 2005
ENCODE: Riken CAGE - predicted gene start sites 13 Sep 2005
ENCODE Gene Prediction Workshop (EGASP) Updates 12 Sep 2005
ENCODE Regions 15 Sep 2004

Human July 2003 (NCBI34/hg16) (hg16, NCBI Build 34)
 
Track/Table Name Release Date
ENCODE EGASP Full (Correction) 12 Jan 2006
ENCODE GIS PET RNA (update) 07 Nov 2005
ENCODE YALE MAS TAR (additional data) 27 Sep 2005
ENCODE YALE MAS RNA (additional data from June freeze) 27 Sep 2005
ENCODE Consensus Unannotated Transfrags 30 Aug 2005
ENCODE All Introns Proximal 17 Jul 2005
ENCODE All Introns Distal 17 Jul 2005
ENCODE All Intergenic Proximal 17 Jul 2005
ENCODE All Intergenic Distal 17 Jul 2005
ENCODE Introns Proximal 17 Jul 2005
ENCODE Introns Distal 17 Jul 2005
ENCODE Intergenic Proximal 17 Jul 2005
ENCODE Intergenic Distal 17 Jul 2005
TBA23 EvoFold (Predictions of RNA Secondary Structure Using TBA23, ENCODE Regions only) 15 Jul 2005
ENCODE Stanford LAGAN Alignments 14 Jul 2005
ENCODE: NHGRI/PSU TBA Alignments 14 Jul 2005
Recombination in 10 ENCODE regions (cM/Mb) 13 Jul 2005
ENCODE Stanford LAGAN Conserved Elements 11 Jul 2005
ENCODE Stanford LAGAN Conservation 11 Jul 2005
Gene Prediction Workshop (EGASP) for Partial ENCODE Regions 06 Jul 2005
Gene Prediction Workshop (EGASP) All ENCODE Regions 06 Jul 2005
ENCODE: Riken CAGE - predicted gene start sites 06 Jul 2005
ENCODE Gene Prediction Workshop (EGASP) Updates 05 Jul 2005
ENCODE HapMap Allele Frequencies 05 Jul 2005
ENCODE: Sanger Assoc 01 Jul 2005
ENCODE: Yale MAS array, RNA Transcriptionally Active Regions, Placenta, Nimblegen Protocol 27 Jun 2005
ENCODE: Yale MAS array, RNA Transcript Map, Placenta, Nimblegen Protocol 27 Jun 2005
ENCODE: Affy RNA Signal, Affy Transfrags, Affy pVal {0,2,8,32}h, Affy Sites {0,2,8,32}h 17 Jun 2005
ENCODE: Yale RNA Transcriptionally Active Regions (TARs) 17 Jun 2005
ENCODE: Yale RNA Transcript Map (Neutrophil, Placenta and NB4 cells) 17 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, P-Values) 15 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Binding Sites) 15 Jun 2005
ENCODE: Boston University ORChID 14 Jun 2005
ENCODE: UC Davis ChIP-chip Nimblegen - E2F1 ab, HeLa Cells 14 Jun 2005
ENCODE: Yale ChIP-chip (STAT1 ab, Hela cells, Signal) 14 Jun 2005
ENCODE: Gencode Introns (Intron validation for selected Gencode Genes) 14 Jun 2005
Gencode Genes (Manual annotations in the ENCODE regions from the Gencode project) 14 Jun 2005
ENCODE: ChIP-PET/GIS (data update, has cluster counts) 14 Jun 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - Pol II, TAF1, AcH3, H3K4me, SUZ12, and H3K27me antibodies - repackage three existing tracks into one 13 Jun 2005
ENCODE: Ludwig Institute/UCSD ChIP-chip - gamma interferon experiments 13 Jun 2005
ENCODE: GIS RNA PET 10 Jun 2005
ENCODE: NHGRI DNaseI-HS (data update; now includes sites from activated as well as unactivated cells) 10 Jun 2005
ENCODE: Sanger ChIP-chip (histones H3,H4 GM06990) 10 Jun 2005
Affymetrix ChIP-chip (Pol2 RA-stim HL60) Signal in ENCODE Regions (changed from wig to bedGraph) 08 Jun 2005
Affymetrix ChIP-chip (Pol2 RA-stim HL60) PValue in ENCODE Regions (changed from wig to bedGraph) 08 Jun 2005
Stanf. Promoter in ENCODE regions (data update; changed to composite track - old name: Promoter/Stanford) 06 Jun 2005
DNA Rep/UVA in ENCODE regions (reloaded with new data) 03 Jun 2005
ChIP-PET/GIS (P53 TFBS in ENCODE regions) 24 May 2005
Promoters/BU (Boston Univ. Promoters in ENCODE regions) 07 May 2005
ENCODE UCSD/Ludwig Chip (acetylated and methylated histone binding) 06 May 2005
ENCODE UCSD Ludwig RNAP, ENCODE UCSD Ludwig TAF1 (tracks combined into composite format) 29 Apr 2005
ChIp/Sanger (Lysine 4 methylation of histone in ENCODE regions) 07 Apr 2005
RNA/Affy Sites (Affymetrix PolyA+ RNA from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) 31 Jan 2005
RNA/Affy Signal (Affymetrix PolyA+ RNA abundance from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) 31 Jan 2005
ChIP Affy Pol2 Sites (Affymetrix ChIP-chip of Pol2 from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) 31 Jan 2005
ChIP Affy Pol2 Pval (Affymetrix ChIP-chip enrichment of Pol2 from retinoic acid-stimulated HL60 cells at 4 timepoints, in ENCODE regions) 31 Jan 2005
ChIP-chip data in ENCODE regions 05 Nov 2004
DNA Rep/UVA (ENCODE DNA Replication data from Dutta Lab, University of VIrginia) 03 Nov 2004
DNaseI-HS/NHGRI (ENCODE DNaseI Hypersensitive sites, from Collins lab, NHGRI) 01 Nov 2004

Mouse Dec. 2011 (GRCm38/mm10) (mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2))
 
Track/Table Name Release Date
GENCODE Gene annotations for mouse, Version M2 11 Mar 2014

Mouse July 2007 (NCBI37/mm9) (mm9, NCBI Build 37)
 
Track/Table Name Release Date
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington (Release 2) 25 Sep 2012
DNaseI Digital Genomic Footprinting from ENCODE/University of Washington 07 Sep 2012
Histone Modifications by ChIP-seq from ENCODE/LICR (Release 3) 05 Sep 2012
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) 05 Sep 2012
Histone Modifications by ChIP-seq from ENCODE/SYDH (Release 2) 20 Aug 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 4) 16 Aug 2012
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU 16 Aug 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR (Release 3) 13 Aug 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU (Release 2) 07 Aug 2012
Histone Modifications by ChIP-seq from ENCODE/PSU (Release 2) 06 Aug 2012
RNA-seq from ENCODE/Stanford/Yale (Release 2) 01 Aug 2012
RNA-seq from ENCODE/UW 10 Jul 2012
Replication Timing by Repli-chip from ENCODE/FSU 03 Jul 2012
Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2) 29 Jun 2012
RNA-seq from ENCODE/Stanford 25 Jun 2012
Mapability or Uniqueness of Reference Genome from ENCODE 19 Jun 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 3) 15 Jun 2012
RNA-seq from ENCODE/Caltech 07 May 2012
RNA-seq from ENCODE/LICR (Release 2) 04 May 2012
Histone Modifications by ChIP-seq from ENCODE/PSU 30 Apr 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR (Release 2) 13 Apr 2012
Histone Modifications by ChIP-seq from ENCODE/LICR (Release 2) 28 Mar 2012
Long RNA-seq from ENCODE/Cold Spring Harbor Lab 29 Feb 2012
Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU 13 Feb 2012
Histone Modifications by ChIP-seq by ChIP-seq from ENCODE/Caltech 28 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech 23 Nov 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 2) 19 Sep 2011
RNA-seq from ENCODE/LICR 04 Aug 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR 22 Jul 2011
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale 22 Jul 2011
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington 01 Jul 2011
Histone Modifications by ChIP-seq from ENCODE/LICR 24 Jun 2011
Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale 07 Feb 2011

Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4, Baylor Release 4.0)
 
Track/Table Name Release Date
ENCODE NHGRI Elnitski Bi-directional Promoters 30 Jul 2009