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Nox1 and Npy1r mark regional colon stem cell populations that serve as cancer origins in vivo [RNA-seq2]

GSE303433 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2025/07/29 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples: 15 conditions, mostly with about 4 replicates eachGroups 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
NOX1 and NPY1R mark regional colon stem cell populations that serve as cancer origins in vivoNature cell biology · 2025
Summary (written by the submitters)
Current colorectal cancer (CRC) mouse models lack either colon specificity, limiting progression towards more advanced disease, or preclude evaluation of resident stem cells as cancer origins. Here, we report identification of Nox1 and Npy1r as cell-surface markers enriched in Lgr5+ stem cells predominantly within the caecum and exclusively within the mid-distal colorectum respectively.
Read the full summary ↓
Selective dysregulation of Wnt signalling in Nox1+ or Npy1r+ stem cells using new CreERT2 mouse lines drives colon cancer initiation, predominantly within the caecum and the rectum respectively, establishing these stem cell populations as important sources of colon cancer. Selective conditional activation of Wnt signalling and oncogenic K-RAS in combination with loss of Trp53 in these stem cell compartments resulted in development of advanced, invasive cancers. This study establishes the new CreERT2 drivers as valuable tools for studying stem cell contributions to colon cancer.
Published in
NOX1 and NPY1R mark regional colon stem cell populations that serve as cancer origins in vivo
Gasnier M, Chen TC, Yada S et al. · Nature cell biology 2025 · PMID 40897804 · doi:10.1038/s41556-025-01763-1
This dataset
Open GSE303433 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 GSE303433_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 PRJNA1295413 and SRA study SRP603168. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40897804) ↗
Study design
15 conditions, mostly with about 4 replicates each
Distal colon, GFP-high, ×4 Distal colon, GFP-intermediate, ×4 Distal colon, GFP-negative, ×4 Proximal colon, GFP-high, ×4 Proximal colon, GFP-intermediate, ×4 Proximal colon, GFP-negative, ×4 Distal small intestine, GFP-high, ×4 Distal small intestine, GFP-intermediate, ×4 +7 more

Supports a between-group comparison across 60 samples.

How we read this: 15 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

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