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Divergent Mechanisms of Tissue Remodeling In Acute and Chronic Models of Allergic Airway Inflammation

GSE288092 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2026/01/14 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 25 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
25 samples: 5 conditions, mostly with about 5 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
Dynamic Regulation of Collagens, Proteases, Their Inhibitors, and Cell Death in Experimental Asthma in MiceAllergy · 2026
Summary (written by the submitters)
Inadequately controlled chronic airway inflammation may result in a series of irreversible changes within lung tissue, referred to as lung remodeling. The increased activation of airway fibroblasts and their differentiation towards myofibroblasts leads to the deposition of extracellular matrix (ECM) components, including collagens. The disrupted balance between the activity and concentration of matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) secreted by structural lung cells and infiltrating immune cells may lead to excessive ECM remodeling.
Read the full summary ↓
Here, we aimed to utilize HDM-induced experimental acute (mixed and neutrophilic) and chronic (neutrophilic) experimental asthma models to assess differences in lower airway remodeling. First, we confirmed increased total collagen deposition within the lung in all analyzed models. Additionally, we found an elevated frequency of IFN-producing T cells in acute neutrophilic inflammation, while an elevated frequency of IL-4 and IL-10-producing T cells was observed in mixed airway inflammation. Transcriptomic analysis revealed Th2- and Th17- -related signaling pathways, while specifically in the chronic model, we noted Th17-driven fibrosis. Moreover, transcriptomic profiling showed the dysregulation in genes associated with ECM morphology, collagens, MMPs, and TIMPs. Targeted protein analysis confirmed the increased deposition of Collagen I, III, IV, and VI. Finally, multiplexing analysis of bronchoalveolar lavage indicated an increase in MMP-2 and TIMP-4 levels among all investigated models, whereas MMP-8 and MMP-9 appeared to be increased explicitly in chronic inflammation. In summary, we confirmed that various inflammatory profiles in experimental asthma models may differentially influence the development of airway remodeling changes.
Published in
Dynamic Regulation of Collagens, Proteases, Their Inhibitors, and Cell Death in Experimental Asthma in Mice
Tynecka M, Tarasik A, Hanczaruk B et al. · Allergy 2026 · PMID 41147134 · doi:10.1111/all.70126
This dataset
Open GSE288092 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 GSE288092_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 PRJNA1216182 and SRA study SRP560105. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41147134) ↗
Study design
5 conditions, mostly with about 5 replicates each
NaCl - 2 weeks ×5 House Dust Mite (HDM) 10 - 2 weeks ×5 House Dust Mite (HDM) 100 - 2 weeks ×5 NaCl - 12 weeks ×5 House Dust Mite (HDM) 100 - 12 weeks ×5

Supports a between-group comparison across 25 samples.

How we read this: 5 replicated groups read from 25 sample titles; they account for 25 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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