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Developmental exposure to air pollution particulates increases asthma severity, alters the RNA transcriptome, and DNA methylation in female adult progeny [RNA-Seq]

GSE285128 Mus musculus (mouse) DNA methylation 23 samples Submitted 2025/03/12 Platform GPL24247
At a glance

DNA methylation · mouse · 23 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
23 samples: 7 × Developmental exposure to PM2.5, no OVA vs 7 × No developmental exposure to PM2.5, no OVA challene vs 5 × No developmental exposure to PM2.5 w/ OVA challenge vs 4 × Developmental exposure to PM2.5 w/ OVA challengeGroups 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
Developmental air pollution exposure augments airway hyperreactivity, alters transcriptome, and DNA methylation in female adult progenyCommunications biology · 2025
Summary (written by the submitters)
Maternal exposure to particulate air pollution increases the incidence and severity of asthma in offspring, yet the mechanisms for this are unclear. Known susceptibility loci are a minor component of this effect. We interrogate a mouse allergic airway disease model to assess epigenetic associations between maternal air pollution exposure and asthma-like responses in offspring.
Read the full summary ↓
Maternal air pollution exposure increased allergic airway disease severity in adult offspring associated with a suppressed transcriptomic response to allergen. Control progeny showed differential expression of 2842 genes across several important pathways, including the SMAD and TGFβR pathways, whilst air pollutant progeny showed an 80% reduction in differentially expressed genes and abrogation of many pathway associations. Whole genome CpG methylome analysis following allergen challenge detected differential methylation regions across the genome. Approximately 20% of differentially expressed genes were associated with differential methylation. Differentially methylated regions were markedly reduced in offspring of air pollution exposed mothers, and this was most evident in intronic regions and some transposable element classes. This study shows that allergic airways disease in adult offspring of PM2.5 exposed mothers had a markedly repressed transcriptomic response, a proportion of which was associated with identifiable changes in the lung’s methylome. The results point to an epigenetic contribution to the severity of asthma in offspring of mothers exposed to particulate air pollution.
Published in
Developmental air pollution exposure augments airway hyperreactivity, alters transcriptome, and DNA methylation in female adult progeny
Zakarya R, Chan YL, Wang B et al. · Communications biology 2025 · PMID 40057553 · doi:10.1038/s42003-025-07835-0
This dataset
Open GSE285128 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 GSE285128_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1201217 and SRA study SRP553056. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40057553) ↗
Study design
7 × Developmental exposure to PM2.5, no OVA vs 7 × No developmental exposure to PM2.5, no OVA challene vs 5 × No developmental exposure to PM2.5 w/ OVA challenge vs 4 × Developmental exposure to PM2.5 w/ OVA challenge

Supports a between-group comparison across 23 samples.

How we read this: 4 replicated groups read from 23 sample titles; they account for 23 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
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