|
| Status |
Public on Jun 06, 2024 |
| Title |
Cultured mouse CAFs_Sen4 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
cell type: Fibroblasts
disease state: PDAC
treatment: Sen
|
| Treatment protocol |
Human and mouse primary CAFs were grown in culture. Senescence was induced by activating a Cre-ER vector that excised hTERT and SV40-LT-Antigen.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted and isolated using TRI reagent (Sigma) and RNA isolation kit (Zymo Research).
Libraries for expression profile were prepared using standard CEL-Seq protocol.
CEL-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
raw_gene_count_Cultured_Mouse.txt
|
| Data processing |
FASTQ files were trimmed and filtered with trim_galore (v0.6.1) for adapter sequences, polyA tails and low quality bases.
Trimmed and filtered reads were mapped with salmon quant function (v1.6.0) to the transcriptome.
Normalization and exploration of differentially expressed genes was perfofrmed with Deseq2 (v1.40.1)
Assembly: hg38 and mm39
Supplementary files format and content: Tab-delimited text file consisting of raw gene counts for each sample.
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Ittai Ben-Porath |
| E-mail(s) |
[email protected]
|
| Organization name |
The Hebrew University Faculty of Medicine
|
| Department |
Department of Developmental Biology and Cancer Research
|
| Street address |
Ein-Kerem
|
| City |
Jerusalem |
| State/province |
N/A |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE235233 |
Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Cultured_Human_Mouse] |
| GSE235246 |
Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma impair CD8+ T cell activation and responsiveness to immunotherapy in mice |
|
| Relations |
| BioSample |
SAMN35801456 |
| SRA |
SRX20726390 |
