This page contains links to directories containing raw and processed data released as part of the ENCODE production phase (September 2007 - December 2012). Formats are described on the File Format FAQ. For bulk download, retrieval by FTP is recommended along with rsync. Using rsync, for example "rsync -a -P rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeDir/wgEncodeFile ./", has the advantage of starting up where it left off after a failure, when ran again. Production data files are covered by the ENCODE data release policy. Links in the blue sections below show descriptions of the data as tracks in the UCSC Genome Browser.

The ENCODE Analysis Working Group (AWG) is a cross-consortium effort to perform integrated analysis of all ENCODE data types based on uniform processing. In September 2012 the results of AWG analysis of data produced from September 2007 through January 2011 were published in a series of coordinated publications. Resulting files from the uniform processing reported in these publications are hosted on the ENCODE Analysis Data Hub for download and visualization in the UCSC Browser. Visit the ENCODE Integrative Analysis and Quality Metrics pages for more information.

Metadata
files.txt	Metadata terms for all Analysis Hub files
cv.ra	Controlled vocabulary used in ENCODE metadata
Uniform Peaks for DNase, FAIRE, Histone, and TFBS
DNase-seq Peaks	DNase-seq Peaks of Open Chromatin
FAIRE Peaks	FAIRE Peaks of Open Chromatin
Histone Peaks	Histone Peaks
TFBS Peaks (SPP)	TFBS SPP-based Peaks
TFBS Peaks (PeakSeq)	TFBS PeakSeq-based Peaks
Uniform Signals for DNase, FAIRE, Histone, and TFBS
Uniform Signals	Signals for DNase-seq, FAIRE, Histone, and TFBS
RNA-seq
RNA-seq Signals	Long and Short RNA-seq Signals
Long RNA-seq Contigs	Long RNA-seq Contigs
Short RNA-seq Contigs	Short RNA-seq Contigs
Other
Genome Segmentations	Genome Segmentations from DNase, FAIRE, Histone and TFBS Signals

Integrated Regulation from UCSC
DNase Clusters	Digital DNaseI Hypersensitivity Clusters from ENCODE
Txn Factor ChIP	Transcription Factor ChIP-seq from ENCODE
Other
Broad ChromHMM	Chromatin State Segmentation by HMM from ENCODE/Broad
Genome Segmentations	Genome Segmentations from DNase, FAIRE, Histone and TFBS Signals
Uniform DNaseI HS	DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis
Uniform TFBS	Transcription Factor ChIP-seq Uniform Peaks from ENCODE/Analysis

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)
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
GIS ChIA-PET	Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan
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.
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
Mappability	Mappability 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
Mappability	Mappability 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