GEO series

Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [mouse_brain_OnurE_RNA-seq]

GSE319252 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/02/11 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × Purified_TBI vs 3 × Purified_Sham vs 3 × FishOil_Sham vs 3 × FishOil_TBIGroups 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)

Repetitive mild traumatic brain injury (rmTBI) precedes chronic traumatic encephalopathy (CTE) and involves neurovascular dysfunction. Omega-3 polyunsaturated fatty acids (PUFA) are promoted as neuroprotective, but long-term effects after brain injury remain uncertain. We uncover a metabolic vulnerability associated with cerebral accumulation of eicosapentaenoic acid (EPA), a major PUFA derived from fish oil.

Read the full summary ↓

In a fish oil diet model, EPA accumulates at baseline yet is selectively depleted after rmTBI, consistent with mobilization during injury-associated metabolic remodeling. This pattern coincides with matrix remodeling, endothelial degeneration, and impaired neurovascular function. Cortical transcriptomics indicates reduced angiogenic programs with increased fatty acid metabolism, and lipidomics links EPA to maladaptive lipid engagement. Mechanistic studies using metabolically adapted endothelial cells show that EPA selectively impairs reparative function. Analysis of postmortem CTE brain tissue reveals parallel vascular and metabolic gene expression changes, strengthening translational relevance. Together, these findings challenge the assumption of uniform omega-3 neuroprotection after brain injury.

This dataset

Open GSE319252 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 GSE319252_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 PRJNA1422697 and SRA study SRP676518. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Purified_TBI vs 3 × Purified_Sham vs 3 × FishOil_Sham vs 3 × FishOil_TBI

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9514292 Purified_TBI2 Purified_TBI
GSM9514293 Purified_TBI3 Purified_TBI
GSM9514294 Purified_TBI4 Purified_TBI
GSM9514295 Purified_Sham2 Purified_Sham
GSM9514296 FishOil_Sham2 FishOil_Sham
GSM9514297 Purified_Sham3 Purified_Sham
GSM9514298 Purified_Sham4 Purified_Sham
GSM9514299 FishOil_TBI2 FishOil_TBI
GSM9514300 FishOil_Sham3 FishOil_Sham
GSM9514301 FishOil_Sham4 FishOil_Sham
GSM9514302 FishOil_TBI3 FishOil_TBI
GSM9514303 FishOil_TBI4 FishOil_TBI

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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.