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ENCODE Project at NHGRI Mouse Downloads

Overview

This page contains links to directories containing raw and processed data for mouse ENCODE data produced as part of the ENCODE production phase (September 2007 - December 2012). Formats are described on the UCSC Browser 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/mm9/encodeDCC/wgEncodeDir/wgEncodeFile ./", has the advantage of starting up where it left off after a failure, when ran again.

Mouse Genome Build NCBI37/mm9

Bidirectional Promoters
NHGRI BiP  NHGRI Elnitski Bidirectional Promoters
Chromatin Accessibility
PSU DNaseI HS DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU
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
Histone Modification
Caltech Histone  Histone Modifications by ChIP-seq from ENCODE/Caltech
LICR Histone  Histone Modifications by ChIP-seq from ENCODE/LICR
PSU Histone  Histone Modifications by ChIP-seq from ENCODE/PSU
Stan/Yale Histone  Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale
Transcription Factor Binding Sites
Caltech TFBS  Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech
LICR TFBS  Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR
PSU TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU
Stan/Yale TFBS  Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale
RNA-seq
Caltech RNA-seq RNA-seq from ENCODE/Caltech
CSHL Long RNA-seq  Long RNA-seq from ENCODE/CSHL
LICR RNA-seq  RNA-seq from ENCODE/LICR
PSU RNA-seq RNA-seq from ENCODE/PSU
Stan/Yale RNA-seq RNA-seq from ENCODE/Stanford
UW RNA-seq RNA-seq from ENCODE/UW
Other
FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU
Mappability Mappability or Uniqueness of Reference Genome from ENCODE