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Cell types activated in mouse muscle by TLR7/8 stimulation

GSE272898 Mus musculus (mouse) Single-cell RNA-seq 23 samples Submitted 2024/09/02 Platform GPL30172
At a glance

Single-cell RNA-seq · mouse · 23 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
23 samples: 23 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
TLR7/8 Activation in Immune Cells and Muscle by RNA-Containing Immune Complexes: Role in Inflammation and the Pathogenesis of MyositisArthritis & rheumatology (Hoboken, N.J.) · 2025
Summary (written by the submitters)
ScRNA-seq analysis of 11,450 cells from mouse muscle tissue sections following R848 injection identified 19 cell clusters, including four fibroblast, two endothelial cell, two macrophage, and two T cell subpopulations. To identify which cell populations were activated downstream of TLR7/8, interferon gene signature (IFN-GS) and NF-κB-gene signature (NF-κB-GS) scores were calculated and heat maps generated.
Read the full summary ↓
There was a noticeable IFN response in most cell populations, with the greatest IFN-GS induction in neutrophils, endothelial cells and macrophages, and some response in T cells. However, IFN induction was not observed in any muscle cell type after R848 injection. The NF-κB-GS was expressed under basal conditions in many cell populations and was induced by R848 most in macrophages and neutrophils, with some increase also seen in endothelial cells.
Published in
TLR7/8 Activation in Immune Cells and Muscle by RNA-Containing Immune Complexes: Role in Inflammation and the Pathogenesis of Myositis
Wu Y, Deshpande A, Geraci N et al. · Arthritis & rheumatology (Hoboken, N.J.) 2025 · PMID 39279150 · doi:10.1002/art.42989
This dataset
Open GSE272898 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 GSE272898_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1139203 and SRA study SRP521721. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39279150) ↗
Study design
23 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 23 sample titles: 23 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.