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Sample GSM886552 Query DataSets for GSM886552
Status Public on Dec 06, 2013
Title 3-APC-iPSC-9 MeDIP sequencing
Sample type SRA
 
Source name APC-iPSC_MeDIPseq
Organism Mus musculus
Characteristics strain: 129-M2rtTA
cell type: APC-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 Genomic DNA was extracted from cell pellets and 5μg original gDNA were prepared for a library. DNA quality was analyzed by Qubit 2.0 Fluorometer (life technologies). gDNA was sonicated to 100-500bp, and repaired to overhang a 3’-dA; then the adapters were ligated to the end of DNA fragments according to the Paired-End DNA Sample Prep Kit (Illumina). For the immunoprecipitation, DNA was first denatured, followed by immunoprecipitated by 5mC antibody using Magnetic Methylated DNA Immunoprecipitation kit (Diagenod). Q-PCR was used to validate the efficiency of the enriched products. Then the pull-down DNA were amplified about 12-15 cycles, and fragments with proper size, usually 200-300bp, were gel-purified using Gel Extraction Kit (Qiagen) and quantified by 2100 Bioanalyzer (Agilent Technologies)
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2000
 
Description Sample 9
Data processing The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_9_peaks.bed: mm9
 
Submission date Mar 06, 2012
Last update date May 15, 2019
Contact name Tao Cai
E-mail(s) caitao@nibs.ac.cn
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)
GSE36293 High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [MeDIP-seq]
GSE36294 High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells
Relations
SRA SRX127418
BioSample SAMN00808857

Supplementary file Size Download File type/resource
GSM886552_medip_9_peaks.bed.gz 2.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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