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ECM29/Proteasome-Mediated Self-Antigen Generation by CNS-Resident Neuroglia Promotes Regulatory T Cell Activation

GSE251784 Mus musculus (mouse) RNA-seq (gene expression) 47 samples Submitted 2024/12/06 Platform GPL19057Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 47 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
47 samples: 12 conditions, mostly in triplicateGroups 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
ECM29/proteasome-mediated self-antigen generation by CNS-resident neuroglia promotes regulatory T cell activationCell reports · 2025
Summary (written by the submitters)
Proteasomes generate antigenic peptides presented on cell surfaces - a process that in neuroglia is highly responsive to external stimuli. However, the function of the self-antigens presented by CNS parenchymal cells remains unclear. Here, we report that the fidelity of neuroglial self-antigens is crucial to suppress encephalitogenic T cell responses via elevating regulatory T cell (Treg) populations.
Read the full summary ↓
We demonstrate that loss of the proteasome adaptor protein Ecm29 alters the efficacy and accuracy of antigen generation. Inducible oligodendroglia- or microglia conditional Ecm29 knockout mice exhibit higher susceptibility of experimental autoimmune encephalomyelitis (EAE) than control counterparts, coincident with reduced Tregs populations in spinal cord. Immunopeptidome profiling identifies self-antigens that modulate myelin-reactive T cell responses. Intraspinal AAV/Olig001-mediated expression of the self-antigen NDUFA1p ameliorated EAE and expands NDUFA1p-recognizing CD103+CD8+CD122+ Tregs. Thus, Ecm29/proteasome-controlled, neuroglia-derived self-antigens modulate CNS immune tolerance.
Published in
ECM29/proteasome-mediated self-antigen generation by CNS-resident neuroglia promotes regulatory T cell activation
Chen SW, Chu Y, Chu CH et al. · Cell reports 2025 · PMID 39786996 · doi:10.1016/j.celrep.2024.115161
This dataset
Open GSE251784 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 GSE251784_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1055460 and SRA study SRP479471. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39786996) ↗
Study design
12 conditions, mostly in triplicate
cspg4-cKO_spinalcord_EAE ×3 pdgfra-cKO_spinalcord_EAE ×3 cx3cr1-cKO_spinalcord_EAE ×3 nestin-cKO_spinalcord_EAE ×3 pdgfra-cKO_lymphnode_EAE ×3 cx3cr1-cKO_lymphnode_EAE ×3 cspg4-cKO_brain_O4+ cell ×2 cspg4-cKO_spinalcord_O4+ cell ×2 +21 more

Supports a between-group comparison across 30 samples.

How we read this: 12 replicated groups read from 47 sample titles; they account for 30 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

+ 7 more — browse all 47 samples with per-sample file links →

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.