|
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 |