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Sample GSM4017155 Query DataSets for GSM4017155
Status Public on Aug 14, 2019
Title ESCs, WT_RNA-seq_rep2
Sample type SRA
 
Source name embryonic stem cell
Organism Mus musculus
Characteristics cell line: E14
genotype: wild type
Growth protocol E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 20% FBS, GlutaMAX (Gibco), MEM Non-Essential Amino Acids (Gibco), Leukemia inhibitory factor, 1 mM sodium pyruvate, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 and 1 mM PD0325901. Cells were cultured at 37 °C under 5% CO2 in air.
Extracted molecule polyA RNA
Extraction protocol Libraries were prepared with TruSeq RNA prep kit (Illumina RS-122-2101).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequence reads were processed with Cutadapt and aligned to mm10 using Tophat.
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: TDF file was generated by using IGV. XLSX file includes FC and false discovery rate (FDR) from edgeR
 
Submission date Aug 08, 2019
Last update date Aug 14, 2019
Contact name Misuzu Kurihara
E-mail(s) kmisuzu1018@gmail.com, miyanari@nibb.ac.jp
Organization name National Institute for Basic Biology
Street address 5-1 Higashiyama, Myodaiji
City Okazaki
State/province Aichi
ZIP/Postal code 444-8787
Country Japan
 
Platform ID GPL17021
Series (2)
GSE135557 RNA-seq analyses of wild-type and PML KO mESCs
GSE135563 Dissecting roles of PML bodies by genome-wide profiling of PML body-associated regions
Relations
BioSample SAMN12532003
SRA SRX6674552

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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