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Sample GSM2433796 Query DataSets for GSM2433796
Status Public on May 29, 2018
Title EpiSC-H3K27me3-ChIP seq
Sample type SRA
 
Source name EpiSC-H3K27me3
Organism Mus musculus
Characteristics cell type: Epiblast stem cells
chip antibody: H3K27me3 (Millipore,07-449)
Growth protocol EpiSCs were maintained on serum-coated plates in chemical defined medium (CDM) supplemented with Activin (20ng/ml) and bFGF (10ng/ml). To derive EpiSCsS/F, EpiSCs were dissociated as small clumps with collagenase IV and replated on serum-coated plates in CDM supplemented with 2μM SB431542 and bFGF (10ng/ml). EpiSCsS/F were passaged using collagenase IV every 2 days. EpiSCsS/F can be cryopreserved using KSR plus 10% DMSO (dimethylsulfoxide) and thawed with similar viability compared with EpiSC.
Extracted molecule genomic DNA
Extraction protocol Cells were collected and fixed in 1% formaldehyde solution and quenched by 0.125M glycine. Fixed cells were fragmented to a size range of 200-500bp by using Bioruptor Pico. Solubilized fragmented chromatin was immunoprecipitated with antibodies.Fragmented DNA was extracted with phenol-chloroform and precipitated with ethanol
DNA fragments acquired from immunoprecipitation would be subjected to end-repaired, adaptor ligation and PCR amplification under the instruction of the manufacturers (New England Biolabs E7370 ).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Raw reads were mapped to mm10 using Bowtie2 version 2.2.2 program
MACS2 version 2.1.1.20160309 was used to call ChIP-seq peaks using broad peak calling mode (with --broad option), as well as to identify differential ChIP-seq signals in different conditions
ChIPseeker was used to annotate ChIP-seq peaks by using the mouse gene annotation GENCODE version M9
deepTools was used to smooth and calculate the ChIP-seq signal as the ratio between ChIP-seq data and corresponding input control data, as well as to visualize ChIP-seq signals.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
 
Submission date Dec 20, 2016
Last update date May 15, 2019
Contact name Naihe Jing
E-mail(s) njing@sibcb.ac.cn
Organization name Shanghai Institute of Biochemistry and Cell Biology
Street address Yue Yang Road 320
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21273
Series (2)
GSE92633 Genome-wide maps of chromatin state in epiblast stem cells and nodal inhibited ebiblast stem cells
GSE92635 Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells
Relations
BioSample SAMN06167401
SRA SRX2437253

Supplementary file Size Download File type/resource
GSM2433796_EpiSC-K27M3_compared.bw 297.1 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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