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Gene expression profile of microglia following traumatic brain injury and adoptive transfer of Tregs at acute and chronic timepoints

GSE276649 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/01/15 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 21 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
21 samples: 6 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
Nasal anti-CD3 monoclonal antibody ameliorates traumatic brain injury, enhances microglial phagocytosis and reduces neuroinflammation via IL-10-dependent T(reg)-microglia crosstalkNature neuroscience · 2025
Summary (written by the submitters)
To investigate whether the immunomodulatory effects of nasal anti-CD3 on the microglial transcriptomic profile following TBI is dependent on Tregs, we employed adoptive transfer experiments
Published in
Nasal anti-CD3 monoclonal antibody ameliorates traumatic brain injury, enhances microglial phagocytosis and reduces neuroinflammation via IL-10-dependent T(reg)-microglia crosstalk
Izzy S, Yahya T, Albastaki O et al. · Nature neuroscience 2025 · PMID 40016353 · doi:10.1038/s41593-025-01877-7
This dataset
Open GSE276649 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 GSE276649_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 PRJNA1155027 and SRA study SRP531275. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40016353) ↗
Study design
6 conditions, mostly with about 4 replicates each
Iso_total_Total_CD4+ ×4 aCD3_FoxP3(ve)GFP ×4 aCD3_Total_CD4+ ×4 TBI_Iso_FoxP3 ×3 TBI_aCD3_FoxP3 ×3 TBI_aCD3_FoxP3Negative ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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
Datasets on a similar topic

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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.