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Sample GSM970225 Query DataSets for GSM970225
Status Public on Dec 05, 2013
Title E36_Eed_+/+_H3K4me1
Sample type SRA
Source name E36 ES cells
Organism Mus musculus
Characteristics strain: 129/Ola
cell type: E36 ES cells
chip antibody: H3K4me1 (Abcam, catNo:8895, Lot: 962543)
Treatment protocol Exponentially growing ES cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using proteinA coupled beads and recovered DNA was used for highthrouput sequencing.
Growth protocol ES cell lines were grown on 0.1% gelatinized tissue culture dishes in GMEM supplemented with 15% fetal calf serum, 2 mM glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin, 0.1 mM non-essential aminoacids, 1 mM Na-Pyruvate, 50 μM β-mercaptoethanol-phosphate-buffered saline and Leukemia Inhibitory Factor.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions accompanying the Illumina ChIPSeq Sample Prep kit (IP-102-1001) and multiplexing oligonucleotide kit (PE-400-1001).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Chromatin precipitatin using a specific antibody against H3K4me1
Data processing Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie. The alignments were performed allowing zero to two mismatches and keeping only the reads that align to unique positions in the genome.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (
Genome_build: mm9
Supplementary_files_format_and_content: Alignment file generated by Bowtie is converted to SAM file format which is compressed to generate BAM file using SAMTools. Wig files generated by MACS were normalized to sequencing depth and converted to bigWig format using UCSC wigToBigwig tool.
Submission date Jul 19, 2012
Last update date May 15, 2019
Contact name Sri Ganesh Jammula
Organization name IFOM-IEO
Street address Via Adamello 16
City Milan
ZIP/Postal code 20139
Country Italy
Platform ID GPL13112
Series (2)
GSE39496 Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E36 with H3K27ac, H3K27me1, and H3K4me1/3)
GSE40118 Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells
SRA SRX160818
BioSample SAMN01091690
Named Annotation GSM970225_E36_Eed_+_+_H3K4me1.bigWig

Supplementary file Size Download File type/resource
GSM970225_E36_Eed_+_+_H3K4me1.bigWig 457.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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