ENCODE at UCSC (2003-2012) - ENCODE Portal (Data 2007-present) - 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.soe.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