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Transcriptomic profiling of the intra-amygdala kainate mouse model across the stages of epileptogenesis

GSE319769 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/04/16 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 6 conditions, mostly with about 6 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
Cross-species transcriptomic analysis of rodent model fidelity to human mesial temporal lobe epilepsyNature communications · 2026
Summary (written by the submitters)
Mesial temporal lobe epilepsy (MTLE) is a prevalent form of drug-resistant epilepsy often associated with hippocampal sclerosis (HS). While various rodent models exist to study this condition, their molecular fidelity to human MTLE requires detailed evaluation. As part of a larger cross-species transcriptomic meta-analysis, we generated this dataset to characterize the intra-amygdala kainate mouse model, which provides a unique framework for studying status epilepticus-induced epileptogenesis.
Read the full summary ↓
We performed bulk RNA-sequencing on hippocampal tissues to capture the evolving molecular landscape during the acute, intermediate, and chronic phases following seizure induction. This dataset allows for the investigation of key epileptogenic processes, including neuroinflammation, neuronal death, and reactive gliosis, and serves as a critical component in comparing chemical induction models against human MTLE pathophysiology.
Published in
Cross-species transcriptomic analysis of rodent model fidelity to human mesial temporal lobe epilepsy
Kim J, Lee S, Kim B et al. · Nature communications 2026 · PMID 42230582 · doi:10.1038/s41467-026-73796-5
This dataset
Open GSE319769 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 GSE319769_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 PRJNA1425071 and SRA study SRP677852. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42230582) ↗
Study design
6 conditions, mostly with about 6 replicates each
iaka3 ×6 iasl3 ×6 iaka7 ×6 iasl7 ×6 iaka14 ×6 iasl14 ×6

Supports a between-group comparison across 36 samples.

How we read this: 6 replicated groups read from 36 sample titles; they account for 36 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

Search all mouse RNA-seq datasets in GEO →

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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.