|
| Status |
Public on Nov 30, 2023 |
| Title |
PSC4_TGFb_2 |
| Sample type |
SRA |
| |
|
| Source name |
PSC4 in control media with 20 ng/mL TGFbeta #2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: PSC4
cell type: Murine pancreatic stellate cells (PSCs)
genotype: WT
agent: TGFbeta
treatment: Day 4
strain: C57BL/6J
passage: p24
|
| Treatment protocol |
PSCs were treated with the conditiones detailed above for 4 days
|
| Growth protocol |
PSCs were grown in Matrigel
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected in 1 mL of TRIzol Reagent and stored at -80C. The RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
mRNA library preparations (Illumina) were performed using 30 µL of 10 ng/mL (300 ng) per sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Estimated transcript counts were counted using Salmon (version 1.4.0)
DEA was performed in R using DESeq package (V2) with default parameters.
GSEA was performed using genes ranked by their p-values using the GSEA program (Broad Institute)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw count data in tab-delimited text format.
|
| |
|
| Submission date |
Dec 01, 2022 |
| Last update date |
Nov 30, 2023 |
| Contact name |
Giulia Biffi |
| E-mail(s) |
Giulia.Biffi@cruk.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Cancer Research UK, Robinson Way
|
| City |
CAMBRIDGE |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE219180 |
RNA-Seq comparison of pancreatic stellate cells (PSCs) cultured with control media, TGF-beta, pancreatic tumor organoid conditioned media or pancreatic tumor organoid conditioned media in the presence of ERBBi (neratinib) |
| GSE243892 |
EGFR-activated cancer-associated myofibroblasts promote metastasis in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN31974942 |
| SRA |
SRX18451479 |
