ENCODE Project at UCSC: Data Release Policy

ENCODE Downloads

This page contains links to directories containing raw and processed data for ENCODE data produced as part of the ENCODE production phase (September 2007-present). For bulk download, retrieval by FTP is recommended. All files here are covered by the ENCODE data release policy.

Human Genome Build 37 (hg19)

Genes
Gencode Genes	Gencode Gene Annotations
RNA-seq
CSHL Sm RNA-seq	Small RNA-seq from ENCODE/Cold Spring Harbor Laboratory
GIS RNA-seq	RNA-seq from ENCODE/Genome Institute of Singapore
Other
GIS DNA PET	Genome Institute of Singapore DNA Paired-End Ditags

Human Genome Build 36 (hg18)

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 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
HAIB TFBS	Transcription Factor Binding Sites by ChIP-seq from HudsonAlpha Institute
Yale TFBS	Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
Other
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