GEO series

Transcriptional dysregulation in the spinal cord of SCA3 provides insights into disease mechanisms

GSE309535 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/10/29 Platform GPL34328

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 8 conditions, mostly in triplicateGroups 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: Early transcriptomic perturbations highlight the spinal cord as a key pathogenic region in spinocerebellar ataxia type 3Frontiers in cellular neuroscience · 2025

Summary (written by the submitters)

Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disease caused by polyglutamine repeat expansion in the ATXN3 gene. Despite the ubiquitous expression of ATXN3 throughout the body, SCA3 pathology is pronounced in select, vulnerable regions within the central nervous system (CNS). Notably, imaging studies of SCA3 patients have revealed spinal cord atrophy prior to ataxia symptom onset and progressing with disease severity.

Read the full summary ↓

However, the molecular mechanisms underlying SCA3 pathology in the spinal cord remain largely unexplored. Here, we present, for the first time, a comprehensive analysis of the spinal cord transcriptome using SCA3 tissue from humans and mouse models. Our data demonstrates both early and progressive transcriptional dysregulation in the spinal cord, impacting key biological processes such as lipid metabolism, inflammation, cellular structure, and nucleic acid processing. Transcriptomic profiling of Atxn3 knockout mice revealed only weak transcriptional changes in the spinal cord, with minimal overlap compared to the robust alterations observed in SCA3 knock-in mice, indicating that the molecular signature of the disease in the spinal cord is likely not driven by ATXN3 loss of function. In addition, we identified aberrant RNA splicing, particularly affecting genes involved in cytoskeletal organization. Collectively, our findings indicate that SCA3-associated transcriptional dysregulation in the spinal cord contributes to canonical pathological mechanisms of SCA3 both early and progressively. These results underscore the central role of the spinal cord in SCA3 pathogenesis and advocate for its inclusion as a key therapeutic target.

Published in

Early transcriptomic perturbations highlight the spinal cord as a key pathogenic region in spinocerebellar ataxia type 3

Emerson J, Nelthrope BS, Walker EA et al. · Frontiers in cellular neuroscience 2025 · PMID 41613623 · doi:10.3389/fncel.2025.1735225

This dataset

Open GSE309535 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 GSE309535_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 PRJNA1336220 and SRA study SRP629643. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41613623) ↗

Study design

8 conditions, mostly in triplicate

KI, M, 24 wk, ×3 WT, F, 24 wk, ×3 WT, M, 24 wk, ×3 KI, F, 24 wk, ×3 WT, M, 56 wk, ×3 WT, F, 56 wk, ×3 KI, F, 56 wk, ×3 KI, M, 56 wk, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM9268811 KI, M, 24 wk, rep1 KI, M, 24 wk,
GSM9268812 KI, M, 24 wk, rep2 KI, M, 24 wk,
GSM9268813 KI, M, 24 wk, rep3 KI, M, 24 wk,
GSM9268814 WT, F, 24 wk, rep1 WT, F, 24 wk,
GSM9268815 WT, F, 24 wk, rep2 WT, F, 24 wk,
GSM9268816 WT, F, 24 wk, rep3 WT, F, 24 wk,
GSM9268817 WT, M, 24 wk, rep1 WT, M, 24 wk,
GSM9268818 WT, M, 24 wk, rep2 WT, M, 24 wk,
GSM9268819 WT, M, 24 wk, rep3 WT, M, 24 wk,
GSM9268820 KI, F, 24 wk, rep1 KI, F, 24 wk,
GSM9268821 KI, F, 24 wk, rep2 KI, F, 24 wk,
GSM9268822 KI, F, 24 wk, rep3 KI, F, 24 wk,
GSM9268823 WT, M, 56 wk, rep1 WT, M, 56 wk,
GSM9268824 WT, F, 56 wk, rep1 WT, F, 56 wk,
GSM9268825 KI, F, 56 wk, rep1 KI, F, 56 wk,
GSM9268826 KI, M, 56 wk, rep1 KI, M, 56 wk,
GSM9268827 WT, M, 56 wk, rep2 WT, M, 56 wk,
GSM9268828 WT, M, 56 wk, rep3 WT, M, 56 wk,
GSM9268829 KI, F, 56 wk, rep2 KI, F, 56 wk,
GSM9268830 KI, M, 56 wk, rep2 KI, M, 56 wk,
GSM9268831 KI, M, 56 wk, rep3 KI, M, 56 wk,
GSM9268832 WT, F, 56 wk, rep2 WT, F, 56 wk,
GSM9268833 WT, F, 56 wk, rep3 WT, F, 56 wk,
GSM9268834 KI, F, 56 wk, rep3 KI, F, 56 wk,

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