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Parkinson's disease (PD) genetic asymmetry in SNCA PFF injected mouse model

GSE266555 Mus musculus (mouse) RNA-seq (gene expression) 64 samples Submitted 2026/05/01 Platform GPL19057
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: 18 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)
We measured gene expression in neuronal nuclei from cortex derived from both hemispheres (injected and noninjected side) of mice (16 male, 16 female) intected with either PBS or SNCA PFFs. Mice were sacrificied at either 1 or 3 month post injection. This was a preliminary experiment done to examine a mouse model of asymmetry in a PD-like condition.
Read the full summary ↓
RNA-sequencing was used to measure gene expression differences resulting from injecting PBS or alpha-synuclein pre-formed fibrils (PFFs), an inducer of PD like neuropathy, in the right olfactory bulb of 32 (C57BL/6J) mice, 16 male and 16 female. Cortex was then isolated for RNA extraction from both right and left hemispherical cortex in all mice at either 1 month or 3-months post-injection. The overall conclusion was that expression changes were found but were too modest to warrant further focus using mice. Greater detail is given below. While the model has some value and the results may be useful for comparison with human data, nuisance variables were found to induce changes of similar magnitude to treatment conditions. The small magnitude in differential expression levels, coupled with strong effects by confounds, primarily cage to cage variation, resulted in less robust results than desirable. Thus, while this pilot experiment indicates that a few dozen to a few hundred genes may show hemispherical asymmetry in the mouse model across sex and timepoint, further experiments will focus on human data. Within the experiment the features conferring the greatest difference in overall gene expression levels between the mice were sex, followed by time post injection (1-month vs. 3-month) (figure 1,2). The conditions of interest, treatment: PBS or PFF, and hemisphere: injected vs non-injected, do not confer obvious structure to overall gene expression patterns. Rather differences between individual mice as well as between cage mates outweigh overall differences for the latter 2 experimental conditions. However, some individual genes do show significant treatment or hemispherical differential expression. This is truer when treatment or hemisphere are considered while holding sex and/or timepoint constant (Table 1). Overall, across 16 statistical comparisons, 1038 statistically significant (FDR < 0.05) and high fold change (>40% change in expression) genes. Of these, excluding simple male vs. female, 342 genes are unique. These 342 genes show enrichment in processes related to neurotransmitter function, especially dopamine, cell signaling, drug binding, complement activation of the immune system, and others. Individual comparisons are expected to be most relevant for elucidating PD asymmetry. For instance, 23 genes are significant (adj. p.value < 0.5 and logFC > 0.5) for differences between injected and non-injected hemispheres regardless of sex or timepoint. These 23 genes show some GO enrichment for axonogenesis and dopaminergic systems, among other things. It is somewhat surprising that such PD-relevant categories show differential expression in this comparison, as the PBS condition should not induce a disease like state. However, the sensitivity of the analysis may be misleading. 2/3 of the significant DE genes were also
This dataset
Open GSE266555 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 GSE266555_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 PRJNA1107579 and SRA study SRP505576. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 conditions, mostly with about 4 replicates each
Male_1_PBS_Injected_C ×4 Male_1_PBS_Non-injected_C ×4 Male_3_PBS_Injected_D ×4 Male_3_PBS_Non-injected_D ×4 Female_1_PBS_Injected_P ×4 Female_1_PBS_Non-injected_P ×4 Female_3_PBS_Injected_Q ×4 Female_3_PBS_Non-injected_Q ×4 +12 more

Supports a between-group comparison across 62 samples.

How we read this: 18 replicated groups read from 64 sample titles; they account for 62 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.