Released Data
| This page lists releases of ENCODE data submitted to the UCSC Genome Browser for data storage and display during the pilot phase of ENCODE (2003 - 2007). Most of these datasets were restricted to the defined ENCODE regions.
Data | Date | Cell Lines
Affy EC RNA (chr21 and chr22) | 16 Apr 2008 | 16 cell lines
Harvard SCONE Cons (update) | 19 Oct 2007 |
BU Orchid (update) | 12 Oct 2007 |
ENCODE hg18 Data Migration and Browser | 8 Oct 2007 |
GIS RNA and ChIP-PET (3 new datasets) | 28 Sept 2007 | ES cells
UC Davis ChIP-chip - Mar07 Batch | 24 July 2007 | HeLa, GM06990
Yale ChIP-chip - Jun07 Batch | 13 Jul 2007 | HeLa
Yale ChIP-chip - Apr07 Batch | 13 Jul 2007 | HeLa
Yale ChIP-chip - Jan07 Batch | 13 Jul 2007 | HeLa, K562
Yale ChIP-chip - Nov06 Batch | 13 Jul 2007 | HeLa, GM06990
Univ. Virginia - Replication Origins (new methods) | 30 May 2007 | HeLa, GM06990
Duke DnaseI HS Feb07 Batch | 21 May 2007 | IMR90, K562, H9
Gencode Genes Mar07 Batch, Gencode RACEfrags | 18 May 2007 |
Gencode RACE Frags | 18 May 2007 |
UC Davis ChIP Hits (E2F1 and c-Myc Peaks update) | 17 Apr 2007 | HeLa
Univ. Virginia DNA Replication Temporal Segmentation (Data correction) | 17 Apr 2007 | HeLa
Sanger ChIP-chip (update, CTCF and 4 histone mods) | 21 Feb 2007 | GM06990
Yale ChIP-chip RFBR | 21 Feb 2007 |
University of Vienna RNA secondary structure predicted by RNAz | 13 Feb 2007 |
UW/Regulome QCP Dnase HS (update and new cell lines) | 7 Dec 2006 | HeLa, GM06990, CD4, K562, HepG2 and 11 others
Duke/NHGRI DNaseI HS (New Chip method) | 5 Dec 2006 | CD4, GM06990, HeLaS3, HepG2
UT-Austin STAGE (STAT1) | 29 Nov 2006 | HeLa S3
Genome Inst. Singapore ChIP/PET (cMyc) | 7 Nov 2006 | P493 B cells
TBA Alignments, Conservation, Elements | 5 Oct 2006 |
MLAGAN Alignments, Conservation, Elements | 5 Oct 2006 |
MAVID Alignments, Conservation, Elements | 5 Oct 2006 |
UCB Alignment Agreement | 5 Oct 2006 |
Conserved Elements (Sep05 MSA freeze) | 5 Oct 2006 |
U North Carolina FAIRE (correction of Peaks data) | 21 Aug 2006 | 2091 fibroblasts
Sanger Chip/Chip in MOLT4 and PTR8 cells | 18 Aug 2006 | HLF-1
University of Uppsala Chip/chip (H3Ac, H4Ac, butyrate treatment) | 26 June 2006 | HepG2
U North Carolina FAIRE (update of Peaks data) | 15 June 2006 | 2091 fibroblasts
UW/Regulome Dnase/Array | 13 June 2006 | GM06990
Sanger Chip/Chip in HLF-1 cells | 24 May 2006 | HLF-1
DLESS (Detection of LinEage Specific Selection) | 19 May 2006 |
Yale ChIP-chip (5 new TFs) | 13 Jan 2006 | HeLa
Yale RNA (update) | 2 Jan 2006 |
University of Uppsala Chip/chip (data correction) | 3 Jan 2006 |
UT-Austin STAGE | 28 Dec 2005 | HeLa
U Virginia DNA Replication Timing and Predicted Origins | 29 Dec 2004 | HeLa
Affy RNA and Transfrags (HeLa update) | 21 Dec 2005 | HeLa
Sanger ChIP-chip (5 histone mods) | 22 Nov 2005 | HeLa, GM06990, K562
U North Carolina FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements | 18 Nov 2005 | 2091 fibroblasts
UC Davis ChIP-chip (Pol2, Myc) | 19 Nov 2005 | HeLa
Affy ChIP-chip (updates and 3 new TFs) | 18 Nov 2005 | HL-60
Affy RNA and Transfrags (update) | 1 Nov 2005 | HL-60, HeLa, GM06990
UT-Austin Ng ChIP-chip (E2F4, c-Myc factors) | 1 Nov 2005 | HeLa, 2091 fibroblasts
GIS PET RNA (update) | 1 Nov 2005 | MCF7 (untreated, and w/ estrogen), HCT116
Gencode Genes and Introns (update) | 1 Nov 2005 |
NHGRI DNaseI HS (update and new GM06990) | 1 Nov 2005 | CD4, GM06990
UCSD/LI Ng ChIP-chip (update and new TFs) | 27 Oct 2005 | HeLa
GIS ChIP/PET (STAT1) | 14 Oct 2005 | HeLa
Boston University ORChID (update) | 21 Sept 2005
TBA23 EvoFold RNA Structure Predictions | 15 July 2005
Regulome DNaseI HS and Sens | 14 July 2005
Regulome Plate Q/A and Amplicons | 14 July 2005
MSA Consensus Elements | 14 July 2005
TBA alignments with Conservation | 14 July 2005
Stanford MLAGAN Alignments and Conservation | 14 July 2005
Oxford Recombination | 13 July 2005
EGASP Genes Full, Partial and Update | 6 July 2005
Stanford DNA Methylation | 6 July 2005
Stanford ChIP-chip and RNA | 6 July 2005
RIKEN FANTOM3 CAGE Tags | 6 July 2005
EGASP Gene Updates | 5 July 2005
HapMap SNP's | 5 July 2005
NHGRI WGS Indels | 1 July 2005
Sanger Association | 1 July 2005
Sanger ChIP-chip update | 1 July 2005
Yale RNA on Nimblegen | 27 June 2005
Affymetrix ChIP-chip and RNA | 17 June 2005
Yale ChIP-chip on multiple arrays | 17 June 2005
Yale RNA on Affy | 17 June 2005
Gencode Genes and Intron Validation | 14 June 2005
UC Davis E2F1 ChIP-chip | 14 June 2005
Boston University ORChID (Hydroxyl Radical Cleavage) | 14 June 2005
UCSD/Ludwig Institute ChIP-chip on Nimblegen | 13 June 2005
UCSD/Ludwig Institute ChIP-chip | 13 June 2005
GIS RNA PET | 10 June 2005
NHGRI DnaseI HS | 10 June 2005
Sanger Histone Modification ChIP-chip (update) | 9 June 2005
Stanford Promoters (update) | 6 June 2005
University of Virginia DNA Replication Timing (update) | 3 June 2005
Genome Institute of Singapore P53 TFBS ChIP/PET | 24 May 2005
Boston University First Exon | 23 May 2005
UCSD/Ludwig Institute Histone Modification ChIP-chip | 6 May 2005
Sanger Histone Modification ChIP-chip | 7 Apr 2005
Affymetrix ChIP-chip and RNA enrichment | 31 Jan 2005
UCSD/Ludwig Institute ChIP-chip | 5 Nov 2004
University of Virginia DNA Replication Timing | 3 Nov 2004
Stanford Promoters | 2 Nov 2004
NHGRI DNaseI Hypersensitive Sites | 1 Nov 2004

Last updated 30 September 2008. Inquiries and feedback welcome.