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. All files here are covered by the ENCODE data release policy.

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
Mapability	Mapability or Uniqueness of Reference Genome from ENCODE