GEO series

Oxidized mitochondrial DNA sensing by plasmacytoid dendritic cells bypasses self-tolerance to trigger Tfh dependent autoantibody production [scRNA-seq]

GSE264620 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/04/10 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 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: 12 samples: 12 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)

Damage associated molecular patterns (DAMP) trigger inflammation and provide co-stimulatory signals to adaptive immune cells, but whether and how recurring innate stimuli circumvent self-tolerance and initiate maladaptive autoimmunity is unknown. We explored if oxidized mitochondrial DNA (Ox-mtDNA), a DAMP released by stressed macrophages, found in higher amounts in diverse metabolic and autoimmune disorders, including systemic lupus erythematosus (SLE), initiates antibody-mediated autoimmunity.

Read the full summary ↓

Indeed, Ox-mtDNA release induced by repetitive alum challenges elicited germinal center reactions, autoantibody production and nephropathology. These responses were recapitulated by in-vitro generated Ox-mtDNA, while non-oxidized mtDNA was non-pathogenic. Both mtDNA forms, but not nuclear DNA, were internalized by plasmacytoid dendritic cells (pDC), activated NF-kB via TLR9 and induced interferon (IFN)-I. Yet only Ox-mtDNA triggered NLRP3- and gasdermin D-dependent IL-1β secretion, eliciting autocrine production of IL-21 that together with IL-1β, but independently of IFN-I, enabled pDC to convert naïve CD4+ T cells into follicular helper cells. Highlighting Ox-mtDNA as a uniquely immunogenic DAMP that is specifically sensed by pDC and IL-1β as an orchestrator of autoantibody production, these findings explain how chronic inflammation culminates in autoimmunity and unravel new therapeutic targets applicable to SLE, the autoimmune/inflammatory syndrome induced by adjuvants (ASIA) and related diseases.

This dataset

Open GSE264620 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 GSE264620_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 PRJNA1103662 and SRA study SRP503691. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 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 12 sample titles: 12 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

GSM8224110 PBS_1_scRNAseq
GSM8224111 PBS_2_scRNAseq
GSM8224112 PBS_3_scRNAseq
GSM8224113 Alum_1_scRNAseq
GSM8224114 Alum_2_scRNAseq
GSM8224115 Alum_3_scRNAseq
GSM8224116 mtDNA_1_scRNAseq
GSM8224117 mtDNA_2_scRNAseq
GSM8224118 mtDNA_3_scRNAseq
GSM8224119 Ox-mtDNA_1_scRNAseq
GSM8224120 Ox-mtDNA_2_scRNAseq
GSM8224121 Ox-mtDNA_3_scRNAseq

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GSE285346 Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity 39 samples shares mitochondrial, dendritic
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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.