Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Kras_p53]
RNA-seq (gene expression) · mouse · 14 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 14 samples: 5 × Kras_Sen vs 3 × Kras_Non-sen vs 3 × Kras+p53_Non-sen vs 3 × Kras+p53_SenGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma restrict CD8(+) T cell activation and limit responsiveness to immunotherapy in miceNature communications · 2024
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE235242_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA985611 and SRA study SRP444829. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 14 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM7497573 Kras_Non-sen1 Kras_Non-sen
- GSM7497574 Kras_Non-sen2 Kras_Non-sen
- GSM7497575 Kras_Non-sen3 Kras_Non-sen
- GSM7497576 Kras_Sen1 Kras_Sen
- GSM7497577 Kras_Sen2 Kras_Sen
- GSM7497578 Kras_Sen3 Kras_Sen
- GSM7497579 Kras_Sen4 Kras_Sen
- GSM7497580 Kras_Sen5 Kras_Sen
- GSM7497581 Kras+p53_Non-sen1 Kras+p53_Non-sen
- GSM7497582 Kras+p53_Non-sen2 Kras+p53_Non-sen
- GSM7497583 Kras+p53_Non-sen3 Kras+p53_Non-sen
- GSM7497584 Kras+p53_Sen1 Kras+p53_Sen
- GSM7497585 Kras+p53_Sen2 Kras+p53_Sen
- GSM7497586 Kras+p53_Sen3 Kras+p53_Sen
- GSE207029 Blockade of avb8 integrin synergizes with checkpoint inhibition to enhance anti-tumor immunity through Cxcl9-dependent augmentation of CD8+ T cell cytotoxicity 12 samples shares cd8, checkpoint
- GSE223164 Osr2 functions as a biomechanical checkpoint to aggravate CD8+ T cell exhaustion in tumor 49 samples shares cd8, checkpoint
- GSE342096 Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence 37 samples shares cd8, activation
- GSE157232 The CD8+ T cell tolerance checkpoint triggers a transcriptionally and epigenetically distinct differentiation state defined by protein translation defects 30 samples shares cd8, checkpoint
- GSE270050 Expansion of Tumor-Infiltrating CD8+ T Cell Clonotypes Occurs in the Spleen in Response to Immune Checkpoint Blockade 29 samples shares cd8, checkpoint
- GSE223157 Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [YODA1_vs_DMSO_ATAC_CD8] 12 samples shares cd8, checkpoint
- GSE270717 The m6A demethylase FTO controls activation-induced cell death in effector CD8+ T cells by modulating Fas expression 10 samples shares cd8, activation
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares adenocarcinoma, pancreatic
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.