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Sample GSM307616 Query DataSets for GSM307616
Status Public on Jul 25, 2008
Title NP_H3K9me3_ChIPSeq
Sample type SRA
 
Source name ES-derived neural precursor cells
Organism Mus musculus
Characteristics Genotype: 129SvJae x C57BL/6
Treatment protocol Described in Mikkelsen et al., Nature 2007
Growth protocol Described in Mikkelsen et al., Nature 2007
Extracted molecule genomic DNA
Extraction protocol Described in Mikkelsen et al., Nature 2007. Briefly, chromatin was fixed in 1% formaldehyde, 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 H3K9me3 (Abcam 8898)
Data processing Described in Mikkelsen et al., Nature 2007. Briefly, sequence reads from each IP experiment were aligned to the mouse reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).
 
Submission date Jul 24, 2008
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9185
Series (1)
GSE12241 Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Relations
SRA SRX001939
BioSample SAMN02195331

Supplementary file Size Download File type/resource
GSM307616_NP.H3K9me3.aligned.txt.gz 94.9 Mb (ftp)(http) TXT
GSM307616_NP.H3K9me3.densities.txt.gz 271.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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