GEO series

Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma

GSE297584 Homo sapiens (human) RNA-seq (gene expression) 11 samples Submitted 2026/03/10 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 11 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: Homo sapiens (human)
Samples: 11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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: Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthmaMucosal immunology · 2026

Summary (written by the submitters)

T cells play a central role in host protection against respiratory pathogens, but a maladaptive T cell response can lead to pulmonary diseases. Defining the biology of protective versus pathogenic T cell responses in the lungs of humans will be critical to nominate novel approaches to improve respiratory health. Previous studies have examined T cells from the lungs captured via bronchoalveolar lavage (BAL), endobronchial brushings, or biopsies.

Read the full summary ↓

However, whether these different approaches are capturing distinct T cell phenotypes and/or clonotypes remains unclear. We aimed to evaluate and compare the transcriptional signatures of T cells isolated via BAL versus endobronchial brushings in healthy controls (HCs) and allergic asthmatics (AAs). The most significant difference in T cell subsets abundance between AAs and HCs was the enrichment of CD4 T helper type 2 (Th2) cells when comparing endobronchial brush samples (OR=26.2, P=0.002), but not when examining BAL (OR=1.7, P=0.46), indicating differences in the T cell subsets captured from the BAL versus airway mucosa specimen processing. TCR repertoire analysis revealed that brush T cells contained dramatically expanded TCR clones. Expanded T cell clones from the brush expressed high levels of resident-memory markers, suggesting the airway mucosa is enriched for TRM cells with unique TCR specificity.

Published in

Distinct phenotypes and repertoires of bronchoalveolar and airway mucosal T cells in health and allergic asthma

Rahimi RA, Smith NP, Selle A et al. · Mucosal immunology 2026 · PMID 41519381 · doi:10.1016/j.mucimm.2026.01.001

This dataset

Open GSE297584 in finder → Find more human 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 GSE297584_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 PRJNA1265215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41519381) ↗

Study design

11 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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

GSM8995180 L0010_brush
GSM8995181 L0012_bal
GSM8995182 L0012_brush
GSM8995183 L0020_bal
GSM8995184 L0020_brush
GSM8995185 L0025_bal
GSM8995186 L0025_brush
GSM8995187 L0031_bal
GSM8995188 L0031_brush
GSM8995189 L0034_bal
GSM8995190 L0034_brush

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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.