GEO series

Single-Cell RNA sequencing reveals clonally-expanded CD4+ tissue-resident memory T cells in Histidyl-tRNA Synthetase-induced myositis [RNA-seq]

GSE336063 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/07/17 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 16 samples: 16 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.

Summary (written by the submitters)

The precise mechanisms underlying the pathogenesis of idiopathic inflammatory myopathy (IIM) remain undefined. However, there has been increasing recognition that tissue-resident memory cells (TRMs) play an important role in the pathogenesis of systemic autoimmune disease. In IIM, TRM-associated transcriptional signatures have been reported, but on a very limited basis.

Read the full summary ↓

By using multimodal single-cell RNA sequencing analysis in our established murine model of histidyl-tRNA synthetase (HRS)-induced myositis, we identified a prominent population of CD4+ TRMs in inflamed skeletal muscle. Muscle CD4+ TRMs exhibited high expression of genes encoding Cd69, Cxcr6, Runx3, and Prdm1, alongside low expression of Klf2, Ccr7, Sell, S1pr1, and Tcf7—a profile that is generally consistent with previous reports of TRM gene signature and that we validate through comparison to transcriptomic profiles of human muscle tissue. Detailed pathway analysis in our model indicates that muscle CD4+ TRMs contribute to innate immune regulatory pathways enriched for TNF and IFN-γ signaling. Furthermore, analysis of TCR clonotype distribution and CDR3 sequence similarity revealed pronounced clonal expansion of CD4⁺ TRMs relative to other T-cell subsets—a pattern that remained stable from 2 to 6 weeks post-immunization. Collectively, these results suggest a potential role for CD4+ TRMs in the pathogenesis of autoimmune myositis.

This dataset

Open GSE336063 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 GSE336063_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 PRJNA1480651 and SRA study SRP711438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 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 16 sample titles: 16 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

GSM9826428 jo1_mice_model_862_ma_inj_lt_hs
GSM9826429 jo1_mice_model_863_ma_inj_lt_hs
GSM9826430 jo1_mice_model_864_ma_inj_lt_hs
GSM9826431 jo1_mice_model_865_ma_inj_lt_hs
GSM9826432 jo1_mice_model_866_ma_inj_lt_hs
GSM9826433 jo1_mice_model_862_pbs_inj_rt_hs
GSM9826434 jo1_mice_model_863_pbs_inj_rt_hs
GSM9826435 jo1_mice_model_864_pbs_inj_rt_hs
GSM9826436 jo1_mice_model_865_pbs_inj_rt_hs
GSM9826437 jo1_mice_model_866_pbs_inj_rt_hs
GSM9826438 jo1_mice_model_867_pbs_inj_rt_hs
GSM9826439 jo1_mice_model_867_pbs_inj_lt_hs
GSM9826440 jo1_mice_model_868_pbs_inj_rt_hs
GSM9826441 jo1_mice_model_868_pbs_inj_lt_hs
GSM9826442 mouse_860_mouse_immunized_with_ma_mbp_fusion_protein_2_3_mg_ml
GSM9826443 mouse_861_mouse_immunized_with_ma_mbp_fusion_protein_2_3_mg_ml

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