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Sample GSM835557 Query DataSets for GSM835557
Status Public on Nov 17, 2012
Title OSKM 2nd 1#-3D
Sample type SRA
 
Source name TSKM-iPS mouse derived fibroblast cells
Organism Mus musculus
Characteristics cell type: fibroblast cells
stage or passages: p4 supply with doxycycline for 3 days
strain: 129/Rosa26-M2rtTA
hmedip: 5hmC
Growth protocol R1 ES cells and iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The O/TSKM 2nd induction cells were derived from O/TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.
Extracted molecule genomic DNA
Extraction protocol In brief, the sonicated genomic DNA was treated using NEBNext master Mix to repair the ends of DNA fragments and ligate the paired-end sequencing specific adaptors (Illumina), the DNA product was then immunoprecipitated and purified. Here we used 500ng ligation product for each IP reaction. Fragments were amplified with 14–16 cycles using adaptor specific primers (Illumina). The final product (300-500bp) was gel-purified (Qiagen) before cluster generation and sequencing.
library strategy: hMeDIP-seq
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina Genome Analyzer IIx
 
Data processing genome build: mm9/ncbi37
 
Submission date Nov 17, 2011
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 GPL11002
Series (1)
GSE33781 Genome-wide maps of 5hmC state in pluripotent and (T-)iPS induction cells.
Relations
SRA SRX105946
BioSample SAMN00759052

Supplementary file Size Download File type/resource
GSM835557_s7_1_map.bed.gz 191.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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