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Sample GSM307605 Query DataSets for GSM307605
Status Public on Jul 25, 2008
Title ESHyb_H3K4me3_ChIPSeq
Sample type SRA
Source name Embyonic Stem Cells (hybrid)
Organism Mus musculus
Characteristics Genotype: 129SvJae x M. m. castaneus F1; Passages 4-6)
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 H3K4me3 (Abcam 8580)
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
SRA SRX001929
BioSample SAMN02195229

Supplementary file Size Download File type/resource
GSM307605_ESHyb.H3K4me3.aligned.txt.gz 289.3 Mb (ftp)(http) TXT
GSM307605_ESHyb.H3K4me3.densities.txt.gz 283.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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