ENCODE at UCSC (2003-2012)   -   Downloads   -   Experiment Summary   -   Experiment Summary   -   Experiment Matrix   -   Experiment Matrix   -   ChIP-seq Matrix   -   ChIP-seq Matrix
ENCODE at UCSC Mouse ENCODE Downloads 2007 - 2012

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