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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 36 (hg18)

Yale TFBS ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard
Broad Histone ENCODE Histone Modifications by Broad Institute ChIP-seq
SUNY RBP ENCODE SUNY Albany RNA Binding Proteins by RIP-chip
Gencode Genes ENCODE Gencode Gene Annotations
HAIB TFBS ENCODE Transcription Factor Binding Sites by ChIP-seq from HudsonAlpha Institute
RIKEN CAGE Loc ENCODE RIKEN RNA Subcellular Localization by CAGE Tags
Open Chromatin ENCODE Open Chromatin, Duke/UNC/UT
Affy RNA Loc ENCODE Affymetrix/CSHL Subcellular RNA Localization by Tiling Array
Helicos RNA-seq ENCODE Helicos RNA-seq
CSHL Long RNA-seq ENCODE Cold Spring Harbor Labs Long RNA-seq
UW DNaseI HS ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI
Common Cell CNV ENCODE Common Cell Type Copy Number Variation, by Illumina 1M and CBS
HAIB Methyl27 ENCODE HudsonAlpha CpG Methylation by Illumina Methyl27
HAIB Methyl-seq ENCODE HudsonAlpha Methyl-seq
NHGRI NRE ENCODE NHGRI Elnitski Negative Regulatory Elements
CSHL Sm RNA-seq ENCODE Cold Spring Harbor Labs Small RNA-seq
UW Affy Exon ENCODE UW Affy All-Exon Arrays
Caltech RNA-seq ENCODE Caltech RNA-seq Map Algorithm
UW Histone ENCODE Histone Modifications by Univ. Washington ChIP-seq
GIS DNA PET ENCODE Genome Institute of Singapore DNA Paired-End Ditags