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Sample GSM470561 Query DataSets for GSM470561
Status Public on Nov 23, 2009
Title h3k27me3_4hr
Sample type SRA
 
Source name mouse bone marrow-derived macrophages
Organism Mus musculus
Characteristics cell type: mouse bone marrow-derived macrophages
treatment: LPS+IFNγ treated for 4 hrs
chip antibody: H3K27me3
Treatment protocol Macrophages were stimulated with lipopolysaccharide (LPS) and interferon gamma (IFNγ)
Growth protocol Primary bone-marrow-derived macrophages were derived from 6-8 week old female Fvb mice as described in (De Santa et al. 2007, PMID: 17825402). Fetal livers were obtained from E14.5 embryos in a mixed L129-C57BL/6 background.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were carried out as described in (De Santa et al. 2007, PMID: 17825402). Libraries for sequencing experiments were generated from 0.5x10^9 cells (Jmjd3) or 1x10^8 cells per point in all other cases. ChIP DNA was ligated to Solexa/Illumina adaptors followed by PCR amplification with limited cycles. The amplified DNA was size selected (~ 200 bp to 300 bp) and subjected to sequencing by Solexa/Illumina protocol. Over 10 million uniquely mapped tags were generated for each ChIP sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K27me3 4 hrs post treatment
Data processing Alignment: Sequence reads were obtained and mapped to the mouse mm8 (February, 2006) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed as described in (Chen et al. 2008, PMID: 18555785)
 
Submission date Nov 13, 2009
Last update date May 15, 2019
Contact name Vipin Narang
Organization name Genome Institute of Singapore
Street address 60 Biopolis Street, #02-01, Genome
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL9185
Series (1)
GSE17631 Genome wide maps of histone demethylase jmjd3, chromatin state and RNA pol in mouse bone marrow-derived macrophages
Relations
SRA SRX012922
BioSample SAMN00005065

Supplementary file Size Download File type/resource
GSM470561_h3k27me3_4hr.peaks.txt.gz 447.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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