|
| Status |
Public on Jun 28, 2023 |
| Title |
SKOV3, DMSO-1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Ovarian Cancer
cell line: SKOV3
genotype: WT
treatment: DMSO
|
| Treatment protocol |
SKOV3 cell line was treated with DMSO and R428 for 24 hrs
|
| Growth protocol |
SKOV3 cell line was maintained using Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) fetal bovine serum (FBS). HeyA8 cell line was maintained using Roswell Park Memorial Institute 1640 media (RPMI) supplemented with 10% (v/v) FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were first harvested by trypsinization and cell pellet was subjected to RNA extraction according to the protocol provided in AllPrep DNA/RNA mini kit (Qiagen). RNA was then quantified using NanoDrop™ 2000 Spectrophotometer. RNA samples were prepared for library preparation at 2.0ug per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Mesenchymal subtype
|
| Data processing |
Reads were mapped to Homo sapiens genome assembly GRCh37/hg19 using STAR alignment software and read counts obtained with RSEM.
Data was filtered to exclude lowly-expressed genes (count per million > 1 in 25% or more samples). Next, data was filtered for known protein-coding genes and normlized using TMM.
Next, data was adjusted for heteroskedasticity using limma package (R version 4.2).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include log2 normalized values for each Sample
|
| |
|
| Submission date |
May 31, 2023 |
| Last update date |
Jun 28, 2023 |
| Contact name |
Tuan Zea Tan |
| E-mail(s) |
csittz@nus.edu.sg
|
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute Singapore
|
| Street address |
14 Medical Drive, #11-01, Singapore
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE233776 |
The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer |
|
| Relations |
| BioSample |
SAMN35539143 |
| SRA |
SRX20546162 |
