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.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeDir/wgEncodeFile ./", has the advantage of starting up where it left off after a failure, when ran again.

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