|
| Status |
Public on Jun 09, 2023 |
| Title |
RNAseqofSUIT2MRTXR:untreated (replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
SUIT2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUIT2
cell type: Pancreatic cancer cell
treatment: untreated
|
| Treatment protocol |
Cells were left untreated or treated with 60 nM MRTX1133 for 24 hours.
|
| Growth protocol |
Parental human SUIT2 or mouse Fc1242 cells and MRTXR human SUIT2 or mouse Fc1242 cells were cultured in 10 cm dishes in duplicate.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted Nucleospin® RNA isolation kit (Macherey-Nagel GmbH & Co.) following the manufacturer’s instructions.
PolyA-enriched RNA libraries were prepared according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
SUIT2_RNAseq.txt
|
| Data processing |
Quality control of the raw fastq files was performed using the software tool FastQC
Sequencing reads were trimmed with Trimmomatic and aligned using the STAR aligner
Read quantification was performed with RSEM
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis
lowly expressed genes—those not having counts per million (cpm) at least 3 in at least 3 of the samples—were filtered out and then trimmed mean of M-values (TMM)10 normalization was applied.
Assembly: GRCh38 for human and GRCm38 for mouse
Supplementary files format and content: SUIT2_RNAseq.txt (tab delimited txt file with nomalized counts)
Supplementary files format and content: FC1242_RNAseq.txt (tab delimited txt file with nomalized counts)
|
| |
|
| Submission date |
Jun 08, 2023 |
| Last update date |
Jun 24, 2023 |
| Contact name |
Herve Tiriac |
| E-mail(s) |
htiriac@health.ucsd.edu
|
| Phone |
8582465564
|
| Organization name |
UCSD Health
|
| Department |
Surgery
|
| Street address |
3855 Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE234449 |
Dual inhibition of KRASG12D and pan-ERBB is synergistic in pancreatic ductal adenocarcinoma |
|
| Relations |
| BioSample |
SAMN35674937 |
| SRA |
SRX20638799 |
