|
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 |