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A developing HPA axis permits neonatal immune sensitivity to common allergens.

GSE299934 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/06/17 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 6 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
Peripheral immune-inducer dendritic cells drive early-life allergic inflammationNature · 2026
Summary (written by the submitters)
Atopic and allergic diseases predominantly manifest in early life, a period of profound growth and maturation. Yet, there is a dearth of information on the impact of developmental parameters on the neonatal immune reaction to allergens. Here we demonstrate that common allergens including house dust mite (HDM) elicited potent type 17 inflammatory responses from neonatal but not adult mice.
Read the full summary ↓
HDM-induced inflammation was abolished in Rorgt-, gd T cell-, or epithelial IL-17RC- deficient animals and surprisingly did not require nociceptors or lymph node engagement. Instead, neonatal CD301b+ type 2 conventional dendritic cells (cDC2s) abundantly engulfed allergen and locally activated gd T cells in the skin. Despite uptaking equivalent antigen to neonates, adult cDC2s did not promiscuously activate in the skin. Mechanistically, this discrepancy was not attributable to cell-intrinsic differences arising from the distinct developmental origins of neonatal and adult cDC2s. Instead, neonatal cDC2 hyperactivation could be traced to a lower systemic glucocorticoid level, a consequence of an immature hypothalamic-pituitary-adrenal (HPA) axis in early life, and could be reversed by cortisol administration at the time of allergen challenge. These findings bring to fore the influence of organismal developmental factors in shaping immune sensitivity to allergens in early life.
Published in
Peripheral immune-inducer dendritic cells drive early-life allergic inflammation
Xing Y, Reznikov I, Ahmed AN et al. · Nature 2026 · PMID 41741647 · doi:10.1038/s41586-026-10162-x
This dataset
Open GSE299934 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 GSE299934_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 PRJNA1277576 and SRA study SRP592683. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41741647) ↗
Study design
6 conditions, mostly with about 4 replicates each
DMSO and HDM treated neonate ×4 Corticosterone and HDM treated neonate ×4 PBS treated adult ×4 HDM treated adult ×4 DMSO and PBS treated neonate ×4 Corticosterone and PBS treated neonate ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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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