|
| Status |
Public on Oct 30, 2015 |
| Title |
mES-control |
| Sample type |
SRA |
| |
|
| Source name |
embronic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embronic stem cell
passages: 17-23
strain: C57BL/6
|
| Growth protocol |
mES cells were routinely generated by re-plating 3-4 days onto fresh MEF-seed dishes in mESC growth medium that consisted of DMEM with high glucose (Hyclone) supplemented with 20% Knockout serum replacement and 1000 U/ml LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA)
The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using bl2fastq version 2.16.0.10
RNA-seq reads were aligned to the mm10 genome using STAR version 2.4.1c using default parameters.
Read counts were obtained with featureCounts using respective gene annotation data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Boyoun Park |
| E-mail(s) |
bypark@yonsei.ac.kr
|
| Organization name |
Yonsei University
|
| Department |
Systems biology
|
| Street address |
50 Yonsei-ro, Seodaemun-gu
|
| City |
Seoul |
| ZIP/Postal code |
120-749 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE74149 |
RNA sequencing analysis in WT and Pc4-OE mESC lines. |
| GSE74156 |
An integrated systems biology approach identifies positive cofactor 4 as a pluripotency regulatory factor |
|
| Relations |
| BioSample |
SAMN04194452 |
| SRA |
SRX1354697 |
