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CD38 endows local antigen-specific Foxp3+ Treg cells with stress resilience for compartmentalized control of CNS inflammation

GSE311963 Mus musculus (mouse) RNA-seq (gene expression) 68 samples Submitted 2025/12/11 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 68 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
68 samples: 16 conditions, mostly with about 4 replicates eachGroups 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
CD38 endows local antigen-specific T(reg) cells with stress resilience for control of compartmentalized CNS inflammationNature immunology · 2026
Summary (written by the submitters)
Foxp3-expressing regulatory T (Treg) cells protect from systemic autoimmunity. However, little is known about the significance of Treg cells in inflammation-experienced tissues. Using experimental autoimmune encephalomyelitis (EAE), we show that Treg cells accumulate and persist in the central nervous system (CNS) until long after the resolution of the bulk of the inflammatory infiltrate.
Read the full summary ↓
CNS-specific local depletion of post-inflammatory Treg cells, but not systemic depletion of Treg cells, immediately rekindles autoimmune inflammatory flares in the CNS by residual local effector T cells. Expression of the NAD-consuming ecto-enzyme CD38 is crucial for the functional adaptation of post-inflammatory CNS Treg cells to a stressful microenvironment, in which access to IL-2 is limited. CD38 counteracts ADP-ribosylation of the IL-2R and, thus, maintains its high sensitivity to IL-2. Their fully functional high-affinity IL-2 receptor prevents the loss of tissue-resident antigen-specific Treg cells. These "stress-tolerant" CNS Treg cells impede the collapse of immune homeostasis in the CNS once acute inflammation is controlled.
Published in
CD38 endows local antigen-specific T(reg) cells with stress resilience for control of compartmentalized CNS inflammation
Chen HH, Tyystjärvi S, Ruiz Navarro D et al. · Nature immunology 2026 · PMID 41611867 · doi:10.1038/s41590-025-02416-z
This dataset
Open GSE311963 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 GSE311963_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 PRJNA1371977 and SRA study SRP650250. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41611867) ↗
Study design
16 conditions, mostly with about 4 replicates each
Murine CNS Tconv from EAE Recovery ×5 Murine CNS Treg from EAE Recovery ×5 Murine Spleen Tconv from EAE Recovery ×5 Murine Spleen Treg from EAE Recovery ×5 Murine CNS Stable Treg from EAE Recovery ×5 Murine CNS Unstable Treg from EAE Recovery ×5 Murine CNS Tconv from EAE Peak ×4 Murine CNS Treg from EAE Peak ×4 +8 more

Supports a between-group comparison across 68 samples.

How we read this: 16 replicated groups read from 68 sample titles; they account for 68 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

+ 28 more — browse all 68 samples with per-sample file links →

Datasets on a similar topic

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