|
| Status |
Public on Sep 30, 2019 |
| Title |
Trog1uM2hrB |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HepG2 cells
passage: 6-8
genotype: ATCC HB-8065
treatment: 1uM Trog, 2hr
|
| Treatment protocol |
Growth media was replaced with serum-free media containing the indicated concentrations of troglitazone or pioglitazone (Sigma-Aldrich) and vehicle (DMSO, 0.1% final concentration), and the treated cells were allowed to grow for 2 or 16 hours.
|
| Growth protocol |
HepG2 cells (ATCC) were cultured in growth media (DMEM supplemented with 1% Penn/Strep, 1% MEM, 1% Glutamax, and 10% Serum) at 37C, 5% CO2 and 85% relative humidity. For treatments, 10^5 cells in 1 ml growth media were seeded into 24-well culture dishes and allowed to settle for 6 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were then stripped of media, washed once with PBS, and were lysed by the addition of 1 ml Trizol. Total RNA was then isolated by Trizol-chloroform extraction, followed by RNeasy cleanup.
3'Pool-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B3
|
| Data processing |
aligned to hg19 reference genome using STAR v2.4
count uniquely aligned reads per gene using FeatureCount from Subread package and gencode v19 as the gene model annotation
Supplementary_files_format_and_content: read counts for each gene in tab delimited format
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Sep 30, 2019 |
| Contact name |
Hualin Xi |
| E-mail(s) |
[email protected]
|
| Organization name |
AbbVie
|
| Street address |
34 webb st
|
| City |
Lexington |
| State/province |
Massachusetts |
| ZIP/Postal code |
02420 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE125570 |
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Glitazone) |
| GSE125571 |
3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling |
|
| Relations |
| BioSample |
SAMN10799683 |
| SRA |
SRX5286778 |
