|
| Status |
Public on Sep 28, 2023 |
| Title |
RAS 4OHT / IMP1088 Day 3, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 ER:RAS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90 ER:RAS
cell type: Lung Fibroblast
genotype: WT
treatment: 4OHT + IMP1088
timepoint: Day 10
|
| Treatment protocol |
IMR90 ER:RAS cells were treated with 100nM 4-OHT (Sigma) or DMSO and then cultured for 7 days before addition of IMP1088 (300nM) or DDD86481 (1.5uM). Cells treated with drugs for 3 days after senescence induction were collected.
|
| Growth protocol |
IMR90 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested by way of Trizol/ Chloroform extraction followed by RNeasy mini plus kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
RAS4OHTIMP1088R2
RAS4OHTIMP1088R2_S53
IMR90 ER:RAS 4OHT + IMP1088
polyA
|
| Data processing |
Primary analysis RTA 3.9.25 and Secondary analysis DRAGEN GenerateFastQ 3.7.4.
Sequencing was conducted on an Illumina NextSeq 2000 system with 71 base pair single-end reads.
Sequencing reads were mapped to hg38 genome using STAR aligner (version 2.7.8a).
Gene based counting was performed using the STAR aligner (version 2.7.8a).
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.32.0).
Assembly: hg38
Supplementary files format and content: Rawcounts.csv: Comma-delimited text file includes raw counts for each Sample generated by STAR aligner.
|
| |
|
| Submission date |
Jan 30, 2023 |
| Last update date |
Sep 28, 2023 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
|
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Bioinformatics Core
|
| Street address |
Hammersmith Hospital Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE224071 |
Effect of NMTi on senescence model systems |
|
| Relations |
| BioSample |
SAMN32961417 |
| SRA |
SRX19215937 |
