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Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus 1 CNS infection

GSE283518 Mus musculus (mouse) Single-cell RNA-seq 20 samples Submitted 2025/06/01 Platform GPL28457
At a glance

Single-cell RNA-seq · mouse · 20 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
20 samples: 6 × Brain stem, D4 post-infection, vs 5 × Brain stem, D6 post-infection, vs 5 × Brain stem, uninfected, vs 4 × Brain stem, D8 post-infection,Groups 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
Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus CNS infectionJournal of neuroinflammation · 2025
Summary (written by the submitters)
We profile the transcriptomic changes in the infected brain stem at the single-cell level with temporal resolution, supported by GeoMx spatial transcriptomic data. Microglia proportions increased during infection, while blood-brain barrier cells declined. Transcriptional analysis revealed strong antiviral and inflammatory responses, and impairment of physiological brain activities. This study highlights the complex immune response in virus-infected brains, balancing infection elimination with immunopathology.
Published in
Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus CNS infection
Ding X, Lai X, Klaestrup IH et al. · Journal of neuroinflammation 2025 · PMID 40450318 · doi:10.1186/s12974-025-03471-x
This dataset
Open GSE283518 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 GSE283518_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 PRJNA1194161 and SRA study SRP549421. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40450318) ↗
Study design
6 × Brain stem, D4 post-infection, vs 5 × Brain stem, D6 post-infection, vs 5 × Brain stem, uninfected, vs 4 × Brain stem, D8 post-infection,

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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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