GEO series

Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of Adam12CKO Mouse Model CD45- cells

GSE313761 Mus musculus (mouse) Single-cell RNA-seq 11 samples Submitted 2025/12/16 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 11 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 11 samples: 3 × MC38, ctrl vs 2 × B16, ctrl vs 2 × B16, CKO vs 2 × MC38, CKOGroups 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.

Summary (written by the submitters)

Clinical trials targeting cancer-associated fibroblasts (CAFs)—crucial pro-tumoral factors in cancer—have almost all failed. This may be ascribed to their intrinsic functional plasticity and the opaque regulatory circuits underlying their heterogeneous phenotypes within tumors. We address these by developing a systematic screening approach for patient-derived fibroblasts using complementary CRISPR interference (CRISPRi) and activation (CRISPRa)-based perturb-seq.

Read the full summary ↓

An anti-tumoral interferon (IFN)-I response-associated program is identified as the primary antagonism axis counteracting TGFβ-driven pro-tumoral myofibroblast activation. ADAM12 emerges as a molecular checkpoint mediating this relationship. Its ablation elicits IFN-I responsive programs, reconfigures myofibroblast population structures into progenitor-like states, revitalizes T cell-based immune responses, and induces tumor rejection across various murine models. Further combined with human genomics data analysis, our findings position ADAM12 as a potential target for fibroblasts, paving the way for actionable therapeutic interventions.

This dataset

Open GSE313761 in finder → Find more mouse RNA-seq datasets →

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 GSE313761_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 PRJNA1381552. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × MC38, ctrl vs 2 × B16, ctrl vs 2 × B16, CKO vs 2 × MC38, CKO

Supports a between-group comparison across 9 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 9 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

GSM9374582 KPC, ctrl
GSM9374583 KPC, CKO
GSM9374584 B16, ctrl1 B16, ctrl
GSM9374585 B16, ctrl2 B16, ctrl
GSM9374586 B16, CKO1 B16, CKO
GSM9374587 B16, CKO2 B16, CKO
GSM9374588 MC38, ctrl1 MC38, ctrl
GSM9374589 MC38, ctrl2 MC38, ctrl
GSM9374590 MC38, ctrl3 MC38, ctrl
GSM9374591 MC38, CKO1 MC38, CKO
GSM9374592 MC38, CKO2 MC38, CKO

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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.