|
| Status |
Public on Apr 05, 2023 |
| Title |
GM21 fibroblasts, pLKO, Day 14 post RAS overexpression rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GM21
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: H-RAS-G12-V overexpression
cell line: GM21
cell type: skin fibroblast
genotype: pLKO
time: Day 14
|
| Treatment protocol |
GM21-RASV12 fibroblasts and their empty vector counterparts were generated by retroviral transduction. GM21 fibroblasts constitutively expressing non-targeting and POU2F2-targeting shRNAs (pLKO.1-Neo-CMV-tGFP, pLKO.1-Neo-CMV-tGFP-TRCN0000245324 and pLKO.1-Neo-CMV-tGFP-TRCN0000245325) (Millipore-Sigma, Saint Louis, MO) were generated by lentiviral transduction and selected with 400 µg/ml neomycin for seven days. Cells were subsequently retrovirally transduced with RASV12
|
| Growth protocol |
Human somatic GM21 foreskin fibroblasts (Coriell Institute, Camden, NJ) and WI-38 human fetal lung fibroblasts (European Collection of Authenticated Cell Cultures, Porton Down, UK) were cultured in a DMEM medium containing 10% fetal bovine serum (FBS) and 1× penicillin/streptomycin (Corning) at 37 °C in a 2% oxygen atmosphere
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Macherey-Nagel RNA XS columns. At least 200 ng RNA with RIN number 9 were used for library construction.
NEB UltraII Directional with poly A selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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: hg19
Supplementary files format and content: BigWig
Supplementary files format and content: tab-delimited text file include normalized counts per Sample
|
| |
|
| Submission date |
Jun 20, 2022 |
| Last update date |
Apr 06, 2023 |
| 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 |
GPL24676 |
| Series (2) |
| GSE206493 |
Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars [RNA-seq] |
| GSE206496 |
Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars |
|
| Relations |
| BioSample |
SAMN29209012 |
| SRA |
SRX15799214 |
