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Sample GSM3168484 Query DataSets for GSM3168484
Status Public on Jun 01, 2019
Title ATAC-seq EB KO re1
Sample type SRA
 
Source name mouse embryonic stem cell
Organism Mus musculus
Characteristics genotype/variation: Trim33 null
strain: C57Bl/6J background ESCs(Xi et al., 2011)
cell type: d2.5 EBs
Treatment protocol Trim33 null ESCs in C57Bl/6J background were cultured on ultra-low plates withdraw LIF and cells were harvested at d2.5
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 Trim33 null ESCs in C57Bl/6J background were cultured on ultra-low plates withdraw LIF and medium were changed every two days, cells were harvested at d2.5
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 After dissociation with Trypsin, embryonic stem cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
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 SAMN09289129
SRA SRX4147801

Supplementary file Size Download File type/resource
GSM3168484_EB_KO_re1_merge2_100bp_rpkm.wig.gz 37.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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