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The gene expression profiles of SOX9+ basal cells (BCs) compared to basal cells during the ALT injury/regeneration process in the surface airway epithelium (SAE).

GSE280283 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/01/30 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 10 × 4ALT, BCAM+ cells, biol vs 6 × 4ALT, BCAM+SOX9-tdTOM+ cells, 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.
Paper
Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programsNature communications · 2026
Summary (written by the submitters)
Tissue-resident stem cells are crucial for repairing barrier tissues that experience frequent damage. However, the local signals that regulate this repair process remain largely unidentified. Here, we show that tuft cell-dependent CysLT activate the LTE4 receptor OXGR1 on SOX9+ accessory stem cells in submucosal glands (SMGs). Activated SMG progenitors regenerate the stem compartment of the SAE, but they also introduce a pro-inflammatory and mesenchymal program, leading to reduced differentiation of ciliated cells.
Read the full summary ↓
This results in ineffective epithelial repair, causing epithelial injury and inflammation. These findings highlight a significant connection between tuft cell sensing of tissue damage and the onset of abnormal wound healing processes observed in the human airway.
Published in
Tuft cells shape airway remodeling by eliciting OXGR1- and SOX9-dependent stem cell programs
Lee M, Wang X, Ye Q et al. · Nature communications 2026 · PMID 41872181 · doi:10.1038/s41467-026-70763-y
This dataset
Open GSE280283 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 GSE280283_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 PRJNA1177523 and SRA study SRP540723. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41872181) ↗
Study design
10 × 4ALT, BCAM+ cells, biol vs 6 × 4ALT, BCAM+SOX9-tdTOM+ cells, biol

Supports a between-group comparison across 16 samples.

How we read this: 2 replicated groups read from 16 sample titles; they account for 16 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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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.