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Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma impair CD8+ T cell activation and responsiveness to immunotherapy in mice

GSE235246 Homo sapiens (human) RNA-seq (gene expression) 38 samples Submitted 2024/06/06 Platform GPL16791Platform GPL17021
At a glance

RNA-seq (gene expression) · human · 38 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
Homo sapiens (human)
Topic
Pancreatic cancerThis series is part of our curated briefing on it.
Samples
38 samples: 10 conditions, mostly with about 4 replicates eachGroups 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma restrict CD8(+) T cell activation and limit responsiveness to immunotherapy in mice
Assouline B, Kahn R, Hodali L et al. · Nature communications 2024 · PMID 39039076 · doi:10.1038/s41467-024-50441-7
This dataset
Open GSE235246 in finder → Find more RNA-seq datasets → Pancreatic cancer landscape →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE235246_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA985592 and SRA study SRP444826. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39039076) ↗
Study design
10 conditions, mostly with about 4 replicates each
Cultured mouse CAFs_Non-sen ×5 Kras_Sen ×5 Cultured human CAFs_Sen ×4 Cultured mouse CAFs_Sen ×4 hPDAC_Non-sen ×4 hPDAC_Sen ×4 Cultured human CAFs_Non-sen ×3 Kras_Non-sen ×3 +2 more

Supports a between-group comparison across 38 samples.

How we read this: 10 replicated groups read from 38 sample titles; they account for 38 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.

Samples in this study
More Pancreatic cancer datasets

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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.