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This page contains links to directories containing raw and processed data for ENCODE data released as part of the ENCODE production phase (September 2007-present). Formats are described on the UCSC Browser File Format FAQ. For bulk download, retrieval by FTP is recommended. All files here are covered by the ENCODE data release policy. Preview of unreleased data for download is available from the Test download server and by FTP. Preview data is made available with the warning that it has not yet been reviewed by UCSC for correctness and is subject to change at any time.

All-Exon Arrays
Duke Affy Exon Affymetrix Exon Array from ENCODE/Duke
UW Affy Exon Affymetrix Exon Array from ENCODE/University of Washington
Chromatin Accessibility
Duke DNaseI HS Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)
GIS ChIA-PET Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
Open Chrom Synth DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA)
UNC FAIRE Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)
UW DNaseI DGF DNaseI Digital Genomic Footprinting from ENCODE/University of Washington
UW DNaseI HS DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
Chromatin Interactions
UMass 5C Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.
UW 5C Chromatin Interactions by 5C from ENCODE/University of Washington
DNA Methylation
HAIB Methyl RRBS DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha
HAIB Methyl450 CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB
Genes
GENCODE Genes V4 GENCODE V4 Gene Annotations
GENCODE Genes V7 Gene Annotations from ENCODE/GENCODE Version 7
GENCODE Genes V10 Gene Annotations from ENCODE/GENCODE Version 10
GENCODE Genes V11 Gene Annotations from ENCODE/GENCODE Version 11
GENCODE Genes V12 Gene Annotations from ENCODE/GENCODE Version 12
Histone Modification
Broad ChromHMM Chromatin State Segmentation by HMM from ENCODE/Broad
Broad Histone Histone Modifications by ChIP-seq from ENCODE/Broad Institute
SYDH Histone Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard
UW Histone Histone Modifications by ChIP-seq from ENCODE/University of Washington
Proteogenomics
UNC/BSU ProtGeno Proteogenomics from ENCODE/Univ. North Carolina/Boise State Univ.
UNC/BSU ProtGenc Proteogenomics and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ.
Regulation Super-track
DNase Clusters Digital DNaseI Hypersensitivity Clusters from ENCODE
Layered H3K27Ac H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE
Layered H3K4Me1 H3K4Me1 Mark (Often Found Near Regulatory Elements) on 7 cell lines from ENCODE
Layered H3K4Me3 H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE
Transcription Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE
Txn Factor ChIP Transcription Factor ChIP-seq from ENCODE
RNA Binding Proteins
SUNY RIP GeneST RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany
SUNY RIP-seq RIP-seq from ENCODE/SUNY Albany
SUNY Tiling RBP Associated RNA by Tiling Array from ENCODE/SUNY Albany
RNA-seq
Caltech RNA-seq RNA-seq from ENCODE/Caltech
CSHL Long RNA-seq Long RNA-seq from ENCODE/Cold Spring Harbor Lab
CSHL Sm RNA-seq Small RNA-seq from ENCODE/Cold Spring Harbor Lab
GIS RNA-seq RNA-seq from ENCODE/Genome Institute of Singapore
HAIB RNA-seq RNA-seq from ENCODE/HAIB
SYDH RNA-seq RNA-seq from ENCODE/Stanford/Yale/USC/Harvard
Subcellular RNA Localization
Affy RNA Loc RNA Subcellular Localization by Tiling Microarray from ENCODE Affymetrix/CSHL
RIKEN CAGE Loc RNA CAGE Subcellular Localization from ENCODE/RIKEN
Transcription Factor Binding Sites
HAIB TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB
SYDH TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard
UChicago TFBS Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago
UTA TFBS Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)
UW CTCF Binding CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington
Other
BU ORChID ORChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius lab)
FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU
GIS DNA PET Genome Institute of Singapore DNA Paired-End Ditags
GIS RNA PET RNA Subcellular Localization by Paired End diTag Sequencing from ENCODE/GIS
HAIB Genotype Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha
Mapability Mapability or Uniqueness of Reference Genome
Stanf Nucleosome Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU
SUNY SwitchGear RNA Binding Protein Associated RNA by SwitchGear from ENCODE/SUNY Albany
UW Repli-seq Replication Timing by Repli-seq from ENCODE/University of Washington
All-Exon Arrays
Duke Affy Exon Duke Affy All-Exon Arrays
UW Affy Exon UW Affy All-Exon Arrays
Chromatin Accessibility
Open Chromatin Open Chromatin, Duke/UNC/UT
UW DNase DGF Univ. Washington Digital DNase Genomic Footprinting
UW DNaseI HS Univ. Washington DNaseI Hypersensitivity by Digital DNaseI
DNA Methylation
HAIB Methyl-seq HudsonAlpha Methyl-seq
HAIB Methyl27 HudsonAlpha CpG Methylation by Illumina Methyl27
Genes
Gencode Genes Gencode Gene Annotations
Histone Modification
Broad ChromHMM Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH
Broad Histone Histone Modifications by Broad Institute ChIP-seq
UW Histone Histone Modifications by Univ. Washington ChIP-seq
Regulation Super-track
DNase Clusters Digital DNaseI Hypersensitivity Clusters
Enhancer H3K27Ac Enhancer and Promoter Histone Mark (H3K27Ac) on 8 Cell Lines
Enhancer H3K4Me1 Enhancer and Promoter Histone Mark (H3K4Me1) on 8 Cell Lines
Promoter H3K4Me3 Promoter Histone Mark (H3K4Me3) on 9 Cell Lines
Transcription Transcription Levels Assayed by RNA-seq on 6 Cell Lines
Txn Factor ChIP Transcription Factor ChIP-seq
RNA-seq
Caltech RNA-seq Caltech RNA-seq Map Algorithm
CSHL Long RNA-seq Cold Spring Harbor Labs Long RNA-seq
CSHL Sm RNA-seq Cold Spring Harbor Labs Small RNA-seq
GIS RNA-seq Genome Institute of Singapore RNA-seq
Helicos RNA-seq Helicos RNA-seq
HudsonAlpha RNA-seq HudsonAlpha RNA-seq
Yale RNA-seq Yale RNA-seq
Subcellular RNA Localization
Affy RNA Loc Affymetrix/CSHL Subcellular RNA Localization by Tiling Array
GIS PET Loc Genome Institute of Singapore Subcellular RNA Localization by Paired End diTag Sequencing
RIKEN CAGE Loc RIKEN RNA Subcellular Localization by CAGE Tags
Transcription Factor Binding Sites
Yale TFBS Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
Other
BU ORChID Boston Univ (Tullius Lab) ORChID Predicted DNA Cleavage Sites
Common Cell CNV Common Cell Type Copy Number Variation, by Illumina 1M and CBS
GIS DNA PET Genome Institute of Singapore DNA Paired-End Ditags
Mapability Mapability or Uniqueness of Reference Genome
NHGRI Bi-Pro NHGRI Elnitski Bidirectional Promoters
NHGRI NRE NHGRI Elnitski Negative Regulatory Elements
SUNY RBP SUNY Albany RNA Binding Proteins by RIP-chip