|
| Status |
Public on Jul 02, 2019 |
| Title |
587587c |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
shRNA: pLKO.1 empty vector
group: Control
|
| Treatment protocol |
IMR90 cells were infected with pLKO.1 GFP or pLKO.1-shRRM2, and 24 hours later cells were infected with pLKO.1 GFP vector or pLKO.1-shp16. Cells were selected with puromycin (3ug/mL) for 7 days.
|
| Growth protocol |
IMR90 were cultured according to the ATCC in low oxygen (2% O2) in DMEM (4.5 g/L glucose, corning cat#10017CV) with 10% FBS supplemented with L-glutamine, non-essential amino acids, sodium pyruvate, and sodium bicarbonate. Experiments were performed on population doubling #30.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with Trizol (Life Technologies) and DNAse treated with RNeasy Mini Kit (Qiagen, cat#74104) following the manufacturer’s instructions.
The cDNA libraries were prepared using KAPA Stranded RNA-Seq Kits with RiboErase (Kapa Biosystems)
Next generation sequencing was performed in The Penn State College of Medicine Genome Sciences and Bioinformatics Core facility using a HiSeq 2500 sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
pLKO.1 empty vector
|
| Data processing |
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using TopHat (v.2.0.9)
Differential expression analysis was done using Cuffdiff tool which is available by Cufflinks (v.2.0.2) as described in (Lynch et al., 2015).
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample and differential expression analysis for Senescnece-bypass Vs Senescence
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Jul 07, 2019 |
| Contact name |
Raquel Buj |
| E-mail(s) |
rbujgomez@pennstatehealth.psu.edu
|
| Organization name |
Penn State College of Medicine
|
| Department |
Physiology
|
| Lab |
Aird
|
| Street address |
500 University Drive
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE133660 |
Gene expression data from IMR90 control, IMR90 shRRM2 and shRRM2/shp16 |
|
| Relations |
| BioSample |
SAMN12175319 |
| SRA |
SRX6386878 |
