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Sample GSM3168493 Query DataSets for GSM3168493
Status Public on Jun 01, 2019
Title H3K27ac ChIP-seq EB SB
Sample type SRA
 
Source name mouse embryonic stem cell
Organism Mus musculus
Characteristics treatment: SB431542 (10 μM, TOCRIS)
genotype/variation: wild type
strain: E14
cell type: d2.5 EBs
antibody: H3K27ac
Treatment protocol differentiatino was induced on ultra-low plates with medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).
Growth protocol E14 WT ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked with 1% formaldehyde at 37 °C for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Then cells were scraped and ChIP was performed and DNA were extracted using a ChIP assay kit (Millipore) as described.
For library construction and sequencing, ChIP-Seq DNA samples were quantified and quality assessed by Qubit 2.0 and Agilent 2100. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample
 
Submission date May 31, 2018
Last update date Jun 01, 2019
Contact name Bofeng Liu
E-mail(s) lbf12thu@gmail.com
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (1)
GSE115169 Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33
Relations
BioSample SAMN09289143
SRA SRX4147810

Supplementary file Size Download File type/resource
GSM3168493_H3k27ac_EB_SB_100bp_rpkm.wig.gz 38.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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