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Sample GSM2587048 Query DataSets for GSM2587048
Status Public on Jul 24, 2017
Title ChIP-Seq analysis of PRDM15 in serum+lif Prdm15KO mES cells replicate 2
Sample type SRA
Source name mESCs cultured in SL
Organism Mus musculus
Characteristics cell type: ESCs
passages: 30-40
strain: C57BL/6
chip antibody: PRDM15 antibody (in house)
Treatment protocol OHT (50nM) 4 days before fixing the cell
Growth protocol Serum+Lif
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
Single read - Illumina
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ES_Prdm15KO_rep2
Data processing Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet –solexa1.3-quals
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from the BAM alignment files, narrowpeak files were generated by MACS 2.0.10
Submission date Apr 24, 2017
Last update date Apr 17, 2020
Contact name Jingxian Zhang
Organization name Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
Department IMCB
Street address 61 Biopolis Drive Proteos
City Singapore
State/province Singpaore
ZIP/Postal code 138673
Country Singapore
Platform ID GPL19057
Series (2)
GSE73692 Genome-wide mapping of PRDM15 binding in pluripotent mouse Embryonic Stem Cells (mESCs)
GSE73694 PRDM15 safeguards naïve pluripotency by transcriptionally regulating WNT and MAPK/ERK signaling
BioSample SAMN06821045
SRA SRX2754636

Supplementary file Size Download File type/resource 143.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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