|
| Status |
Public on Jul 22, 2024 |
| Title |
WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WI38 (ATCC,CCL-75 )
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WI38 (ATCC,CCL-75 )
cell type: normal lung fibroblasts
genotype: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT
treatment: 4-OHT
time: 144hrs
|
| Treatment protocol |
WI38-ER:RAS(G12V) cells were generated via retroviral transduction and were stimulated to with 400 nM 4-hydroxytamoxifen (4-OHT). Samples were collected and processed at indicated time-points post 4-OHT treatment.
|
| Growth protocol |
WI38 normal human lung fibroblasts (CCL-75, ATCC) were cultured in a DMEM (D629, Sigma) medium supplemented with 10% fetal bovine serum (#25-514, GenClone) at 37°C in a 5% CO2 and 2% O2 atmosphere.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Macherey-Nagel RNA Plus XS columns (#740990.250)
NEB UltraII Directional with poly A selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Description |
Rep1-D6-4OHT
|
| Data processing |
fastq files were quality checked with multiqc
fastq files were aligned using bowtie 2 with the local option in paired-end mode
read counts per exon were obtained using summarized overlaps
count normalization was performed using DESeq2
Assembly: GRCh38-hg38
Supplementary files format and content: BigWig
Supplementary files format and content: tab-delimited text file include normalized counts per sample
|
| |
|
| Submission date |
Jul 03, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Ricardo Iván Martínez Zamudio |
| E-mail(s) |
rm1238@rwjms.rutgers.edu
|
| Organization name |
Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School
|
| Department |
Pharmacology
|
| Lab |
Martínez Zamudio Lab
|
| Street address |
675 Hoes Lane West
|
| City |
Piscataway |
| State/province |
New Jersey |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE271461 |
Transcription factor network dynamics during the commitment to oncogene-induced senescence [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN42288836 |
| SRA |
SRX25202404 |
