|
| Status |
Public on Oct 26, 2020 |
| Title |
WT_GS_1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblast(MEF)
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Pontin WT
media: Glucose starvation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extraction was performed using Trizol (Invitrogen) and RNA-seq library was generated using the Illumina TruSeq method according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina True-seq RNA sample prep kit v2, according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the mm9 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D).
read counts were obtained for each sample for RNA-seq data.
The reads were normalized (based on Generalized Linear Models ) using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including CPM for each sample
|
| |
|
| Submission date |
Apr 19, 2019 |
| Last update date |
Oct 26, 2020 |
| Contact name |
Young Suk Yu |
| Organization name |
Seoul National University
|
| Street address |
1-Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE130069 |
mRNA profiling of Pontin WT and RA under glucose starvation |
|
| Relations |
| BioSample |
SAMN11466852 |
| SRA |
SRX5712386 |
