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Transcriptional Dysregulation in the Hippocampus of a Mouse Model for Parkinson's - Linked Cognitive Decline is Driven by Sex, Age, and Alpha-synuclein overexpression

GSE271598 Mus musculus (mouse) RNA-seq (gene expression) 64 samples Submitted 2025/04/01 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 64 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
64 samples: 16 conditions, mostly with about 4 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.
Summary (written by the submitters)
Cognitive decline is the most common and detrimental non-motor symptom of Parkinson’s disease (PD), and is an understudied disease entity. Pathologically, cognitive decline in PD is associated with alpha-synuclein (aSyn) misfolding and synapse loss in hippocampus and prefrontal cortex, leading to cognitive impairment and, ultimately, dementia.
Read the full summary ↓
The mechanisms of cognitive decline and the factors driving them in PD are unknown. In the present study, we have used longitudinal gene expression profiling to characterise hippocampal molecular events in a transgenic mouse overexpressing E46K mutated aSyn, a model of early PD. Uncovering early events leading to disease is an essential step toward prognostic biomarker identification and early interventions. Transgenic aSyn induced synaptophysin loss in hippocampus and cortex of these mice. Comparing 4 different ages of mice from both sexes uncovered that hippocampal gene expression changes are sexually dimorphic and strongly modulated by the age, and by aSyn overexpression. Pathways that emerged across different comparisons were connected to a variety of neuronal functions, collagen synthesis/remodeling, cellular stress, and inflammatory responses. The findings indicate that sex and age are essential factors to consider when studying PD-associated cognitive decline. This may have important implications for prognostic biomarker identification and monitoring, and for timing of therapeutic approaches.
This dataset
Open GSE271598 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 GSE271598_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 PRJNA1132271 and SRA study SRP518204. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly with about 4 replicates each
HET_F_14M ×4 WT_F_14M ×4 HET_M_14M ×4 WT_M_14M ×4 WT_M_3M ×4 HET_M_3M ×4 HET_F_3M ×4 WT_F_3M ×4 +8 more

Supports a between-group comparison across 64 samples.

How we read this: 16 replicated groups read from 64 sample titles; they account for 64 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

+ 24 more — browse all 64 samples with per-sample file links →

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.