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Sample GSM3168497 Query DataSets for GSM3168497
Status Public on Jun 01, 2019
Title RNA-seq KO 1 SB2h
Sample type SRA
 
Source name mouse embryonic stem cell
Organism Mus musculus
Characteristics treatment: SB431542 (10 μM, TOCRIS)
genotype/variation: Trim33 null
strain: C57Bl/6J background ESCs(Xi et al., 2011)
cell type: d2.5 EBs
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 Trim33 null ESCs in C57Bl/6J background 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 total RNA
Extraction protocol Total RNA purified from d2.5 EBs with Trim33 null ESCs in C57Bl/6J background (as described (Xi et al., 2008) was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000
The RNA-seq library preparation and sequencing was performed as descripted before (Wang et al.,2017)
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNA-seq_FPKM_list.xlsx
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 GPL17021
Series (1)
GSE115169 Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33
Relations
BioSample SAMN09289139
SRA SRX4147814

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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