GEO series

Bacteroides Fragilis enterotoxin engagement of the colonic epithelium is associated with early YAP1 activation and colon tumorigenesis

GSE334603 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/06/10 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × Min ET, biol vs 3 × Min YAPKO ET, biol vs 3 × Min YAPKO Sham, biol vs 3 × Min Sham, biolGroups 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)

Enterotoxigenic Bacteroides fragilis (ETBF) promotes colonic inflammation and tumorigenesis, but the epithelial signaling events linking toxin (BFT2)-induced junctional injury to tumor development remain incompletely defined. Here, wild-type BFT2, but not catalytically inactive BFT2, induced E-cadherin loss and nuclear accumulation of active YAP1 in colonic epithelial cells.

Read the full summary ↓

Deletion of BFT receptors, CLAUDINs 3 and 4 mitigated BFT-associated E-cadherin loss and YAP1 nuclear translocation, supporting a model in which BFT epithelial targeting is linked to early YAP1 activation. In ETBF-colonized Min mice, epithelial YAP1 activation was rapid and transient, whereas STAT3 and NF-kB activation persisted after colonization. Nevertheless, conditional deletion of epithelial Yap1 was sufficient to abrogate colon tumor formation without altering ETBF colonization or abolishing IL-17 colitis. Transcriptomic analyses further associated epithelial Yap1 deficiency with reduced regenerative epithelial programs and increased secretory-cell differentiation signatures. Together, these findings support a model in which BFT engagement of CLAUDINs and toxin catalytic activity are associated with epithelial YAP1 activation, and epithelial YAP1 contributes to ETBF-associated colon tumorigenesis in Min mice

This dataset

Open GSE334603 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 GSE334603_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 PRJNA1476026 and SRA study SRP707593. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Min ET, biol vs 3 × Min YAPKO ET, biol vs 3 × Min YAPKO Sham, biol vs 3 × Min Sham, biol

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

GSM9791629 Min ET, biol rep 1 Min ET, biol
GSM9791630 Min ET, biol rep 2 Min ET, biol
GSM9791631 Min ET, biol rep 3 Min ET, biol
GSM9791632 Min YAPKO ET, biol rep 1 Min YAPKO ET, biol
GSM9791633 Min YAPKO ET, biol rep 2 Min YAPKO ET, biol
GSM9791634 Min YAPKO ET, biol rep 3 Min YAPKO ET, biol
GSM9791635 Min YAPKO Sham, biol rep 1 Min YAPKO Sham, biol
GSM9791636 Min YAPKO Sham, biol rep 2 Min YAPKO Sham, biol
GSM9791637 Min YAPKO Sham, biol rep 3 Min YAPKO Sham, biol
GSM9791638 Min Sham, biol rep 1 Min Sham, biol
GSM9791639 Min Sham, biol rep 2 Min Sham, biol
GSM9791640 Min Sham, biol rep 3 Min Sham, biol

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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.