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Sample GSM886494 Query DataSets for GSM886494
Status Public on Dec 06, 2013
Title 2-HPC-iPSC-16 input DNA
Sample type SRA
Source name HPC-iPSC input DNA
Organism Mus musculus
Characteristics strain: 129-M2rtTA
cell type: HPC-derived induced pluripotent stem cells
passage: 10-12
Growth protocol ES cells and iPS cells were maintained in ES cell media containing 15% FBS and 1,000 Uml-1 of LIF.MEF and APCs were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. HPCs was freshly isolated from bone marrow
Extracted molecule genomic DNA
Extraction protocol 1.5x108 cells were resuspended in lysis buffer and digested with micrococcal nuclease about 5 minutes at 37℃.Then, the lysate was immunoprecipitated with antibody anti-H3K4me2, anti-H3K4me3, anti-H3K27me3; meanwhile, retaining a fraction of input ‘whole-cell extract’ as sequencing control. Immunoprecipitation-enrichment of chromatin fragments were defined and the bound DNA were purified using phenol:chloroform extractions. Chiped DNA was quantified by Qubit 2.0 Fluorometer (life technologies) and Q-PCR was performed to validate the enrichment efficiency. Then the enriched DNA was sonicated to 100-500bp fragments. DNA-end was repaired to overhang a 3’-dA, then adapters was ligated to the end DNA fragments. DNA fragments about 100-300bp, were recovered and amplified to construct the sequencing library. Thirty-nine ChIP library and thirteen input controls were used for sequencing.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Sample 4
Data processing The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Submission date Mar 06, 2012
Last update date May 15, 2019
Contact name Tao Cai
Organization name National Institute Of Biological Sciences, Beijing (NIBS)
Lab Sequencing Facility
Street address No. 7 Science Park Road, Zhongguancun Life Science Park
City Beijing
ZIP/Postal code 102206
Country China
Platform ID GPL13112
Series (2)
GSE36292 High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [ChIP-seq]
GSE36294 High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells
SRA SRX127360
BioSample SAMN00808798

Supplementary data files not provided
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Raw data are available in SRA
Processed data not provided for this record

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