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Sample GSM397406 Query DataSets for GSM397406
Status Public on Jun 06, 2009
Title H3K27me3_ChIP-Seq_XT67E1_4d-atRA
Sample type SRA
 
Source name Embryonic Stem cells
Organism Mus musculus
Characteristics strain: C3H/Pgk*129
cell type: ES-cells
antibody: H3K27me3 from T. Jenuwein
Treatment protocol ES cells were either treated with atRA for 4 days or grown to EBs (removal of LIF) for 10 days
Growth protocol ES cells were cultured in normal cell culture containing ES-grade serum supplemented with LIF. These cells were grown on gelatin-coated plates
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K27me3
Data processing Reads (32 bp) were aligned to the Mouse (Mus muscules) reference genome. Tracks for the different cell lines or antibodies were equalized for the total number of mapped tags by random removal of sequenced tags. Wiggle files were generated from these bed files.
All ChIP-Seq sequence analyses were conducted based on Mus musculus NCBI m37 genome assembly (MM9) accessed from the Ensembl (release 49) or the UCSC (assembly July 2007) genome browsers.
 
Submission date Apr 24, 2009
Last update date May 15, 2019
Contact name H.G. Stunnenberg
E-mail(s) h.stunnenberg@ncmls.ru.nl
Phone +31-24-3610520
Organization name Radboud University
Department Department of Molecular Biology (274)
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country USA
 
Platform ID GPL9185
Series (2)
GSE15814 High resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq
GSE15884 High resolution analysis of epigenetic changes associated with X inactivation
Relations
SRA SRX006972
BioSample SAMN02197751
Named Annotation GSM397406_XT67E1_4d-atRA_H3K27me3-ChIP-Seq.wig.gz

Supplementary file Size Download File type/resource
GSM397406_XT67E1_4d-atRA_H3K27me3-ChIP-Seq.bed.gz 54.5 Mb (ftp)(http) BED
GSM397406_XT67E1_4d-atRA_H3K27me3-ChIP-Seq.wig.gz 17.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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