GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE31039 Query DataSets for GSE31039
Status Public on Jul 30, 2011
Title Histone Modifications by ChIP-seq from ENCODE/LICR
Project Mouse ENCODE
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yin Shen If you have questions about the Genome Browser track associated with this data, contact ENCODE (

This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq (Robertson et al., 2007) to identify transcription factor binding sites and chromatin modification profiles in many mouse (C57Bl/6) tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.
In specific, the Ren lab examined RNA polymerase II (PolII), co-activator protein p300, the insulator protein CTCF, and two chromatin modification marks H3K4me3 and H3K4me1 due to their demonstrated utilities in identifying promoters, enhancers and insulator elements (Barski et al., 2007; Blow et al., 2010; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005a; Visel et al., 2009). Enrichment of H3K4me3 or PolII signals is a strong indicator of active promoter, while the presence of p300 or H3K4me1 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million monoclonal, uniquely mapped tags.

For data usage terms and conditions, please refer to and
Overall design Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev/ENCODE/protocols/cell/mouse).
Enrichment and Library Preparation: Chromatin immunoprecipitation was performed according to Ren Lab ChIP Protocol (
Library construction was performed according to Ren Lab Library Protocol (
Sequencing and Analysis: Samples were sequenced on Illumina Genome Analyzer II Genome Analyzer IIx, and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts.
Web link
Contributor(s) Ren B, Shen Y
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA63471
Submission date Jul 29, 2011
Last update date May 15, 2019
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (133)
GSM769008 LICR_ChipSeq_ES-Bruce4_H3K4me3
GSM769009 LICR_ChipSeq_ES-Bruce4_H3K4me1
GSM769010 LICR_ChipSeq_ES-Bruce4_Input
SRA SRP007600

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE31039_RAW.tar 7.1 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK)
GSE31039_run_info.txt.gz 1.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap