|
| Status |
Public on Jul 06, 2023 |
| Title |
shp15-3_S4 |
| Sample type |
SRA |
| |
|
| Source name |
COLO-357 (metastatic pancreatic adenocarcinoma)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PDAC cell line COLO-357
genotype: CDKN2B (p15) silencing
treatment: shRNAs against p15
|
| Treatment protocol |
Cells were transfected using Jet Pei (Polyplus Transfection, France). Lentiviral infection was conducted as described (Zinger L, Merenbakh-Lamin K, Klein A, et al. Ligand-binding Domain-activating Mutations of ESR1 Rewire Cellular Metabolism of Breast Cancer Cells. Clin Cancer Res 2019;25:2900-2914).
|
| Growth protocol |
Cells were grown in DMEM containing 10% fetal bovine serum (FBS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction, library preparation and sequencing were conducted as previously described (Boldes T, Merenbakh-Lamin K, Journo S, et al. R269C variant of ESR1: high prevalence and differential function in a subset of pancreatic cancers. BMC Cancer 2020;20:531).
as previously described (Boldes T, Merenbakh-Lamin K, Journo S, et al. R269C variant of ESR1: high prevalence and differential function in a subset of pancreatic cancers. BMC Cancer 2020;20:531).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S4
|
| Data processing |
Partek Flow (build 8.0.19.0610).
Trim bases based on quality score, min Phred score 20.
STAR - 2.6.1d aligned to hg38.
Quantify to annotation model (Partek E/M). Gene level qualntifiaction, RPKM normalization.
Genome_build: hg38
Supplementary_files_format_and_content: gene_rpkm_07012020_1-12.xls
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Metsada Pasmanik-Chor |
| E-mail(s) |
metsada@tauex.tau.ac.il
|
| Organization name |
Tel Aviv University
|
| Department |
Biology
|
| Lab |
Bioinformatics Unit
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE154492 |
Genomic alterations drive metastases formation in pancreatic ductal adenocarcinoma cancer: deciphering the role of CDKN2A and CDKN2B in mediating liver tropism |
|
| Relations |
| BioSample |
SAMN15543619 |
| SRA |
SRX8737140 |
