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Transcriptional profiling of cDC2 subsets in IFNAR∆CD11c mice treated with allergens

GSE276029 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/07/21 Platform GPL30172
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: 8 conditions, mostly in triplicateGroups 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
Interferon signaling in type-2 dendritic cells supports T(H)2 and T follicular helper fates in response to allergensImmunology and cell biology · 2025
Summary (written by the submitters)
Conventional type 2 Dendritic Cells (cDC2) in the skin are cell subsets primarily responsible for the priming of T-helper type 2 (TH2) responses in the draining LN. The local inflammatory milieu has been demonstrated to condition cDC2 to promote such responses. To characterise the cDC2 response to the cytokine IFN-I, we performed bulk RNAseq on sorted cDC2 subsets from IFNAR∆CD11c and IFNARWT mice following treatment with an allergen.
Published in
Interferon signaling in type-2 dendritic cells supports T(H)2 and T follicular helper fates in response to allergens
Webb GR, Hilligan KL, Old SI et al. · Immunology and cell biology 2025 · PMID 40462316 · doi:10.1111/imcb.70035
This dataset
Open GSE276029 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 GSE276029_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 PRJNA1154305 and SRA study SRP529501. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40462316) ↗
Study design
8 conditions, mostly in triplicate
Wildtype, CD11bhi, Nippo, ×3 Wildtype, CD11blo, Nippo, ×3 IFNAR^flox/flox; CD11c-Cre, CD11bhi, Nippo, ×3 IFNAR^flox/flox; CD11c-Cre, CD11blo, Nippo, ×3 Wildtype, CD11bhi, PBS, ×3 Wildtype, CD11blo, PBS, ×3 IFNAR^flox/flox; CD11c-Cre, CD11bhi, PBS, ×3 IFNAR^flox/flox; CD11c-Cre, CD11blo, PBS, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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
Datasets on a similar topic

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