GEO series

Distinct Autoreactive CD19– Plasma Cell Subsets Accumulate in Lupus

GSE275094 Mus musculus (mouse) Single-cell RNA-seq 15 samples Submitted 2025/10/01 Platform GPL13112

At a glance

Single-cell RNA-seq · mouse · 15 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: 15 samples: 15 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: Distinct autoreactive CD19(-) plasma cell subsets accumulate in lupus-prone miceNature communications · 2025

Summary (written by the submitters)

Plasma cells (PCs) play a pathogenic role in autoimmune diseases by secreting autoantibodies and inflammatory cytokines. While PC elimination therapies exist, they risk depleting protective long-lived plasma cells. Using single cell RNA sequencing, including B cell receptor repertoire analysis, and genetic models, we identified disease- and organ-specific PC subsets in systemic lupus erythematosus (SLE) mice.

Read the full summary ↓

We uncovered a substantial expansion of autoreactive CD19– PCs, particularly switched CXCR3+ and phosphatidylcholine-specific B-1-derived subsets, which exhibit unique gene expression profiles in SLE. Notably, our findings suggest that CD19– PCs originate from CD19+ PCs in a unidirectional manner, complicating the effectiveness of CD19-targeted therapies in advanced disease stages. This study highlights the crucial role of timing in anti-CD19 therapy and the necessity to broaden therapeutic targets beyond CD19+ PCs. The emergence of CD19– subpopulations underscore the need for novel therapeutic strategies that target these elusive PCs, offering new avenues for intervention in SLE treatment.

Published in

Distinct autoreactive CD19(-) plasma cell subsets accumulate in lupus-prone mice

Dang VD, Szelinski F, Mohr E et al. · Nature communications 2025 · PMID 41213970 · doi:10.1038/s41467-025-65906-6

This dataset

Open GSE275094 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 GSE275094_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 PRJNA1149093 and SRA study SRP526952. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41213970) ↗

Study design

15 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 15 sample titles: 15 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

GSM8465565 BM_healthy, GEX
GSM8465566 BM_healthy, ADT
GSM8465567 BM_healthy, BCR
GSM8465568 BM_sick, GEX
GSM8465569 BM_sick, ADT
GSM8465570 BM_sick, BCR
GSM8465571 spleen_healthy, GEX
GSM8465572 spleen_healthy, ADT
GSM8465573 spleen_healthy, BCR
GSM8465574 spleen_sick, GEX
GSM8465575 spleen_sick, ADT
GSM8465576 spleen_sick, BCR
GSM8465577 kidney_sick, GEX
GSM8465578 kidney_sick, ADT
GSM8465579 kidney_sick, BCR

Datasets on a similar topic

GSE306514 Chemokine receptor expression patterns delineate distinct interstitial macrophage subsets in the lung and define a trajectory from monocytes to mature macrophages, bulk RNA-sequencing data 24 samples shares distinct, subsets
GSE273420 Splenic FO B and MZ B cells from Rack1(f/f) and Rack1(f/f;CD19-Cre) mice were sorted and subjected to bulk RNA-seq 11 samples shares cd19
GSE235325 In vivo single-cell CRISPR uncovers distinct TNF-α programs in tumor evolution 256 samples shares distinct
GSE280652 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 42 samples shares distinct
GSE205411 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations 2219 samples shares distinct
GSE205991 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [deep single-cell RNA-seq] 2148 samples shares distinct
GSE243289 Induction of a distinct macrophage population and protection from lung injury and fibrosis by Notch2 blockade 30 samples shares distinct
GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares distinct

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.