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The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [RNA-Seq]

GSE234316 Mus musculus (mouse) RNA-seq (gene expression) 87 samples Submitted 2025/01/16 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 87 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
87 samples: 34 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
The meninges host a distinct compartment of regulatory T cells that preserves brain homeostasisScience immunology · 2025
Summary (written by the submitters)
Our knowledge about the meningeal immune system has recently burgeoned, particularly how innate and adaptive effector cells are mobilized in response to brain challenges. However, information on how meningeal immunocytes guard brain homeostasis in healthy individuals remains sparse. This study highlights the heterogeneous and polyfunctional regulatory T (Treg) cell compartment in mouse meninges.
Read the full summary ↓
A Treg subtype specialized in controlling Th1-cell responses and another subtype devoted to controlling responses in B-cell follicles were substantial components of this compartment, foretelling the finding that punctual Treg-cell ablation rapidly unleashed interferon-gamma production by meningeal lymphocytes, unlocked their access to the brain parenchyma, and altered meningeal B-cell profiles. Distally, the hippocampus took on a reactive state, with activation of multiple glial-cell types; within the dentate gyrus, neural stem cells showed exacerbated death and desisted from further differentiation, associated with inhibition of spatial-reference memory. Thus, meningeal Treg cells are a multifaceted bulwark to brain homeostasis at steady-state.
Published in
The meninges host a distinct compartment of regulatory T cells that preserves brain homeostasis
Marin-Rodero M, Cintado E, Walker AJ et al. · Science immunology 2025 · PMID 39873623 · doi:10.1126/sciimmunol.adu2910
This dataset
Open GSE234316 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 GSE234316_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 PRJNA980745 and SRA study SRP441405. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39873623) ↗
Study design
34 conditions, mostly in triplicate
Treg.meninges# ×3 Treg.spleen# ×3 skull.BM# ×3 Microglia.DTR-# ×3 Meninges.IgG# ×3 Men.72.DTR-# ×3 Men.DTR+# ×3 Hippocampus.DTR+# ×3 +26 more

Supports a between-group comparison across 87 samples.

How we read this: 34 replicated groups read from 87 sample titles; they account for 87 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

+ 47 more — browse all 87 samples with per-sample file links →

Datasets on a similar topic

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