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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