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Sample GSM985055 Query DataSets for GSM985055
Status Public on Dec 11, 2013
Title E36_Eed_+/+_H3
Sample type SRA
Source name E36 ES cells
Organism Mus musculus
Characteristics cell line: E36
strain: 129/Ola
chip antibody: H3
antibody vendor/catalog/lot: Abcam/No 1791/GR50122-1
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 H3
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.
Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (
Genome_build: mm9
Submission date Aug 14, 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)
GSE40109 Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells (E14 and E36 with H3K27me1/2 and H3)
GSE40118 Polycomb-dependent H3K27me1 and H3K27me2 characterization in mouse ES cells
SRA SRX176651
BioSample SAMN01113287
Named Annotation GSM985055_E36_Eed_+_+_H3.bigWig

Supplementary file Size Download File type/resource
GSM985055_E36_Eed_+_+_H3.bigWig 506.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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