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Effects of hypoxia on brain gene expression in a mouse model of Parkinson’s disease

GSE296779 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2025/07/14 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 12 × Substantia nigra, PFF, normoxia, vs 12 × Substantia nigra, PFF, hypoxia, vs 12 × Substantia nigra, monomer, hypoxia, vs 12 × Substantia nigra, monomer, normoxia,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
Hypoxia ameliorates neurodegeneration and movement disorder in a mouse model of Parkinson's diseaseNature neuroscience · 2025
Summary (written by the submitters)
The purpose of this study was to evaluate whether chronic, continuous hypoxia (breathing 11% FIO2) would improve neurodegenerative disease in a mouse model of Parkinson's disease, which was modeled through intrastriatal injection of a-synuclein preformed fibrils (PFFs). We find that chronic, continuous hypoxia helps to prevent further neurodegeneration and alleviate neurological disease.
Published in
Hypoxia ameliorates neurodegeneration and movement disorder in a mouse model of Parkinson's disease
Marutani E, Miranda M, Durham TJ et al. · Nature neuroscience 2025 · PMID 40770507 · doi:10.1038/s41593-025-02010-4
This dataset
Open GSE296779 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 GSE296779_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 PRJNA1261049 and SRA study SRP584292. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40770507) ↗
Study design
12 × Substantia nigra, PFF, normoxia, vs 12 × Substantia nigra, PFF, hypoxia, vs 12 × Substantia nigra, monomer, hypoxia, vs 12 × Substantia nigra, monomer, normoxia,

Supports a between-group comparison across 48 samples.

How we read this: 4 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.