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Sample GSM703186 Query DataSets for GSM703186
Status Public on Oct 17, 2013
Title Sox2 ChIP-seq, Oct3/4KO Day0
Sample type SRA
Source name ZHBTc4 ES cells, untreated
Organism Mus musculus
Characteristics strain: 129/Ola
cell line: ZHBTc4
treatment: control
time: 0 day
chip antibody: Sox2 produced in-house
condition: On MEF feeders
Treatment protocol TS cells were induced in GMEM/10% FBS supplemented with 1 ug/ml Tet, 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.
Growth protocol ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on gelatin-coated dishes.
Extracted molecule genomic DNA
Extraction protocol Chromatin was enzymatically sheared into fragments with an average size of 300-500 bp using the ChIP-IT Express Enzymatic Kit (Active Motif). Sequencing libraries were prepared from ChIP DNA according to the manufacturer's protocols. Briefly, ChP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-400 bp and amplified by 18 cycles of PCR.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against Sox2
Data processing Basecalls performed using CASAVA version 1.8.2. Sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 with default parameters. Sequence reads overlapping with repetitive sequences were removed using BedTools and repeat region data from UCSC Genome Browse. Peak Calling was performed using MACS2 with input DNA as a control and with a q-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2. The signals were normalized by sequencing depth of million mapped reads with the --SPMR option.
Submission date Apr 07, 2011
Last update date May 15, 2019
Contact name Itoshi NIKAIDO
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
Platform ID GPL11002
Series (2)
GSE28453 Dynamics of Sox2 and Esrrb occupancy during the differentiation of embryonic stem cells into trophoblast stem cells.
GSE28455 Sox2-regulatory networks in embryonic and trophoblast stem cells
SRA SRX057755
BioSample SAMN00259680

Supplementary file Size Download File type/resource 50.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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