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Perturb-seq experiment on patient-derived cancer-associated fibroblast in vitro cell line models from pancreatic ductal adenocarcinoma

GSE306853 Homo sapiens (human) Single-cell RNA-seq 70 samples Submitted 2025/09/12 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 70 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
Pancreatic cancerThis series is part of our curated briefing on it.
Samples
70 samples: 12 conditions, mostly in duplicateGroups 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
In vitro models of cancer-associated fibroblast heterogeneity uncover subtype-specific effects of CRISPR perturbationsMolecular oncology · 2026
Summary (written by the submitters)
Cancer-associated fibroblasts (CAFs) are sought after as potential therapeutic targets due to their plethora of pro- and antitumorigenic functions. Recent findings attributed this functional heterogeneity to specializations in CAF subtypes. A precise targeting of specific subtypes would thus be required to design therapies that effectively modulate CAF phenotypes, but our knowledge of CAF heterogeneity in solid tumors, particularly pancreatic ductal adenocarcinoma (PDAC), is still lacking.
Read the full summary ↓
Here, we use single-cell transcriptomics to characterize CAF subtype heterogeneity in in vitro CAF cell lines isolated from pancreatic tumor patients and investigate subtype-resolution modulations arising from perturbing potential stromal genes. We use the immortalized CAF cell lines to perform single-cell CRISPR perturbations of candidate stromal targets, revealing not only the subtype-specific effects of the perturbations, but also the impact of model-type selection on the translatability of insights.
Published in
In vitro models of cancer-associated fibroblast heterogeneity uncover subtype-specific effects of CRISPR perturbations
Saputra E, Vellarikkal SK, Li L et al. · Molecular oncology 2026 · PMID 41146557 · doi:10.1002/1878-0261.70153
This dataset
Open GSE306853 in finder → Find more human 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 GSE306853_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1299397 and SRA study SRP605510. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41146557) ↗
Study design
12 conditions, mostly in duplicate
hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×12 hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×12 hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×10 hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×10 hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×7 hTERT-immortalized PDAC CAFs, BxPC3 co-cultur… ×7 hTERT-immortalized PDAC CAFs, monoculture, mR… ×2 hTERT-immortalized PDAC CAFs, monoculture, sg… ×2 +4 more

Supports a between-group comparison across 70 samples.

How we read this: 12 replicated groups read from 70 sample titles; they account for 70 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

+ 30 more — browse all 70 samples with per-sample file links →

More Pancreatic cancer datasets

Search all human RNA-seq datasets in GEO →

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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.