GEO series

Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium [Figure 5]

GSE287341 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/04/28 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × Vehicle vs 3 × TGFB1 vs 3 × Vehicle_Tgfbr2KO vs 3 × TGFB1_KOGroups 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: Dynamic Reprogramming of PDGFRA-Expressing Stromal Cells Facilitates WNT-Driven Transformation by Promoting a Fetal-Like State in the Intestinal EpitheliumCancer research · 2026

Summary (written by the submitters)

Stromal fibroblasts of the mesenchyme regulate critical signaling gradients along the crypt-villus axis1 and provide a niche that supports intestinal stem cells in the intestine. Here we report that Pdgfra-expressing fibroblasts secrete ligands that promote a fetal-like state in the intestinal mucosa during early WNT-mediated tumorigenesis.

Read the full summary ↓

Using a mouse model of WNT-driven oncogenesis and single-cell RNA sequencing (RNA-seq) of mesenchyme cell populations, we revealed a dynamic reprogramming of Pdgfra+ fibroblasts that facilitates WNT-mediated tissue transformation. Functional assays of potential mediators of cell-to-cell communication between these fibroblasts and the oncogenic epithelium revealed that TGFB signaling is notably induced in Pdgfra+ fibroblasts in the presence of oncogenic epithelium, and TGFB was essential to sustain fetal-like growth of organoids ex vivo. Genetic reduction of Cdx2 in the β-catenin mutant epithelium elevated the fetal-like transcriptome and accelerated WNT-dependent onset of oncogenic transformation of the tissue in vivo. These results demonstrate that Pdgfra+ fibroblasts are activated during WNT-driven oncogenesis to promote a fetal-like state in the epithelium that precedes and facilitates formation of tumors.

Published in

Dynamic Reprogramming of PDGFRA-Expressing Stromal Cells Facilitates WNT-Driven Transformation by Promoting a Fetal-Like State in the Intestinal Epithelium

Pellon-Cardenas O, Rout P, Hassan S et al. · Cancer research 2026 · PMID 41784677 · doi:10.1158/0008-5472.CAN-25-0101

This dataset

Open GSE287341 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 GSE287341_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 PRJNA1212161 and SRA study SRP558130. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41784677) ↗

Study design

3 × Vehicle vs 3 × TGFB1 vs 3 × Vehicle_Tgfbr2KO vs 3 × TGFB1_KO

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8744552 Vehicle Rep 1 Vehicle
GSM8744553 Vehicle Rep 2 Vehicle
GSM8744554 Vehicle Rep 3 Vehicle
GSM8744555 TGFB1 Rep 1 TGFB1
GSM8744556 TGFB1 Rep 2 TGFB1
GSM8744557 TGFB1 Rep 3 TGFB1
GSM8744558 Vehicle_Tgfbr2KO Rep 1 Vehicle_Tgfbr2KO
GSM8744559 Vehicle_Tgfbr2KO Rep 2 Vehicle_Tgfbr2KO
GSM8744560 Vehicle_Tgfbr2KO Rep 3 Vehicle_Tgfbr2KO
GSM8744561 TGFB1_KO Rep 1 TGFB1_KO
GSM8744562 TGFB1_KO Rep 2 TGFB1_KO
GSM8744563 TGFB1_KO Rep 3 TGFB1_KO

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