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Subclinical Neonatal HSV-1 Infection Triggers Immune Responses and Modulates Neurological Pathways Leading to Long-Term Sequelae

GSE299440 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2026/07/01 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 7 × whole mouse brain 7 DPI 100 PFU HSV-1 sample vs 5 × whole mouse brain 7 DPI Mock sample vs 4 × whole mouse brain 5 WPI 100 PFU HSV-1 sample vs 4 × whole mouse brain 5 WPI Mock sampleGroups 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.
Summary (written by the submitters)
Subclinical neonatal infections represent a poorly understood but potentially critical determinant of long-term neurodevelopmental outcomes. Here, we show that neonatal exposure to herpes simplex virus type 1 (HSV-1), even in the absence of overt symptoms, induces persistent transcriptional and cellular changes in the brain that correlate with anxiety-like behavior later in life.
Read the full summary ↓
Neonatal mice were subclinically infected intranasally with HSV-1 and assessed at acute (3 days post-infection) and chronic (5–6 weeks post-infection) stages using cytokine profiling, bulk RNA sequencing, and spatial transcriptomics. We observed sustained elevation of immune mediators, including CXCL10, IL-6, and IL-10, at both acute and chronic stages. Bulk RNA-seq analysis identified over 490 differentially expressed genes, with distinct expression modules that diverged significantly between early and late infection phases. Notably, several modules exhibited minimal acute changes but showed pronounced dysregulation chronically, highlighting a temporal evolution in gene expression extending beyond the initial immune response. Spatial transcriptomic analysis at the acute phase demonstrated region-specific dysregulation in pathways involving MAPK signaling, chemokine signaling, axon guidance, and long-term depression. These changes were localized to brain regions critical for affective regulation, including the midbrain, hypothalamus, and alar thalamus. Cell-type deconvolution of bulk RNA-seq data further revealed an increased abundance of astrocytes and microglia, underscoring the early involvement of glia in neuroimmune responses. Collectively, our findings illustrate that clinically silent neonatal HSV-1 infection induces spatially and temporally distinct transcriptional alterations in the developing brain. This study provides mechanistic insights into the relationship between early-life viral exposure and long-term modifications in neural circuitry and behavior, highlighting the developmental vulnerability of the neonatal brain to subclinical immune perturbations.
This dataset
Open GSE299440 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 GSE299440_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 PRJNA1274443 and SRA study SRP591061. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 × whole mouse brain 7 DPI 100 PFU HSV-1 sample vs 5 × whole mouse brain 7 DPI Mock sample vs 4 × whole mouse brain 5 WPI 100 PFU HSV-1 sample vs 4 × whole mouse brain 5 WPI Mock sample

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
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