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Sample GSM281695 Query DataSets for GSM281695
Status Public on Jul 06, 2008
Title ES_H3K4me1_ChIPSeq
Sample type SRA
Source name Embyonic stem cells (V6.5)
Organism Mus musculus
Characteristics Chromatin IP against H3K4me1
Growth protocol ES cells were cultured under standard conditions in the presence of LIF; NPCs were derived dy directed differentiation in the presence of Fgf2 (see Meissner et al., 2008)
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 Antibody: H3K4me1
Data processing Described in Meissner et al, 2008. 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 Apr 14, 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)
GSE11172 Genome-wide chromatin state maps of ES cells, ES-derived neural progenitor cells and brain tissue
SRA SRX000583
BioSample SAMN02195368

Supplementary file Size Download File type/resource
GSM281695_ES.H3K4me1.aligned.txt.gz 149.9 Mb (ftp)(http) TXT
GSM281695_ES.H3K4me1.densities.txt.gz 258.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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