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Timing-dependent neuroprotection of dexamethasone in neonatal hypoxic-ischemic brain injury mouse model : Transcriptomic insights into synaptic signaling and calcium homeostasis

GSE325742 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2026/06/18 Platform GPL13112
At a glance

RNA-seq (gene expression) · mouse · 15 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
15 samples: 5 × control vs 5 × pre vs 5 × postGroups 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
Timing-Dependent Effects of Dexamethasone in a Mouse Model of Neonatal Hypoxic-Ischemic Brain Injury: A Transcriptomic Analysis of Synaptic Signaling and Calcium HomeostasisInternational journal of molecular sciences · 2026
Summary (written by the submitters)
Background: Neonatal hypoxic–ischemic (HI) brain injury is a leading cause of neurodevelopmental disabilities. While dexamethasone has shown potential neuroprotective effects, its molecular mechanisms and the optimal timing of administration remain incompletely understood. Main body: In this study, we investigated the neuroprotective effects of dexamethasone pretreatment in a neonatal hypoxic–ischemic brain injury model and explored the underlying molecular mechanisms using next-generation sequencing (NGS).
Read the full summary ↓
Neuropathological analysis demonstrated that dexamethasone pretreatment attenuated brain injury. Differentially expressed genes (DEGs) were identified based on an adjusted p-value (FDR) < 0.05 using the Benjamini–Hochberg correction. A total of 962 DEGs were identified, including 407 upregulated and 555 downregulated genes. Functional enrichment analysis revealed that upregulated genes were primarily associated with central nervous system development, synaptic signaling, and ionic homeostasis, whereas downregulated genes were mainly involved in cellular metabolic processes. Protein–protein interaction network analysis further demonstrated that DLG4, CALM1, and GRIN1 were highly interconnected within the enriched signaling pathways. Conclusion: Our findings demonstrate that dexamethasone provides time-dependent neuroprotection by stabilizing synaptic networks and modulating metabolic demand. These results highlight the critical importance of early intervention and provide a molecular framework for developing pharmacological strategies against neonatal HI injury
Published in
Timing-Dependent Effects of Dexamethasone in a Mouse Model of Neonatal Hypoxic-Ischemic Brain Injury: A Transcriptomic Analysis of Synaptic Signaling and Calcium Homeostasis
Lim J, Han J, Shin JE et al. · International journal of molecular sciences 2026 · PMID 42278447 · doi:10.3390/ijms27114920
This dataset
Open GSE325742 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 GSE325742_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 PRJNA1441549 and SRA study SRP685998. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42278447) ↗
Study design
5 × control vs 5 × pre vs 5 × post

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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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