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Transcriptomic profiling of Sox11 wildtype and mutant intestinal organoids upon treatment with TGF-β1

GSE278490 Mus musculus (mouse) Single-cell RNA-seq 32 samples Submitted 2025/05/20 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 32 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
32 samples: 16 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
TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoidsOncogenesis · 2025
Summary (written by the submitters)
Colorectal cancer (CRC) cells infiltrating surrounding tissue commonly undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and possibly interconnected remains underexplored. Here, we used intestinal organoids with CRC driver mutations as model system to investigate the mechanistic basis of TGF‑β1-induced pEMT and collective invasion.
Read the full summary ↓
By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype in human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF‑β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated Sox11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several, distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.
Published in
TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoids
Teng YH, Appiah B, Andrieux G et al. · Oncogenesis 2025 · PMID 40393982 · doi:10.1038/s41389-025-00560-7
This dataset
Open GSE278490 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 GSE278490_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 PRJNA1167625 and SRA study SRP535891. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40393982) ↗
Study design
16 conditions, mostly in duplicate
Sox11_WT_KO_RNA_seq, 931-TKA, KO3, solvent, b… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, KO3, TGF-β1, bi… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, KO17, solvent, … ×2 Sox11_WT_KO_RNA_seq, 931-TKA, KO17, TGF-β1, b… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, NT6, solvent, b… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, NT6, TGF-β1, bi… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, Par, solvent, b… ×2 Sox11_WT_KO_RNA_seq, 931-TKA, Par, TGF-β1, bi… ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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
Datasets on a similar topic

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