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Autoantibody-induced arthritis pain caused by a sustained type I interferon signaling

GSE218634 Mus musculus (mouse) Single-cell RNA-seq 26 samples Submitted 2025/12/10 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 26 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
26 samples: 11 conditions, mostly in duplicateGroups 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
Persistent interferon signaling causes sensory neuron plasticity and pain before and during arthritisNature neuroscience · 2026
Summary (written by the submitters)
Pain in rheumatoid arthritis is highly debilitating, impacts quality of life and lacks adequate treatment options. Although the presence of pathogenic autoantibodies and systemic and joint inflammation are distinctive features of the disease, the molecular and neuronal basis of pain remains unclear. Here, we identify the molecular mechanism and causative neurons for autoantibody-induced pain in mice.
Read the full summary ↓
Single-cell RNA sequencing analysis during arthritis pain revealed interferon-stimulated genes, with a persistent nociceptor neuron sensitization, local inflammation and a causative role of interferons acting on polymodal GFRa3-positive C-fiber-nociceptors, as the origin of pain. Consistently, interferon inhibition blocked gene expression alterations and prevented onset as well as reversed established and residual arthritis pain. The discovered pain-causative mechanism may represent a novel therapeutic approach for treatment of pain in rheumatoid arthritis.
Published in
Persistent interferon signaling causes sensory neuron plasticity and pain before and during arthritis
Su J, Zhang MD, Kupari J et al. · Nature neuroscience 2026 · PMID 41807847 · doi:10.1038/s41593-026-02234-y
This dataset
Open GSE218634 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 GSE218634_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 PRJNA904728 and SRA study SRP409485. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41807847) ↗
Study design
11 conditions, mostly in duplicate
DRG, control, timepoint 0, scRNAseq ×4 DRG, RA, timepoint 0.5d, scRNAseq ×4 DRG, RA, timepoint 1d, scRNAseq ×2 DRG, RA, timepoint 2d, scRNAseq ×2 DRG, RA, timepoint 0.25d, scRNAseq ×2 DRG, RA, timepoint 12d, scRNAseq ×2 DRG, RA, timepoint 33d, scRNAseq ×2 DRG, RA, timepoint 63d, scRNAseq ×2 +3 more

Supports a between-group comparison across 26 samples.

How we read this: 11 replicated groups read from 26 sample titles; they account for 26 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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