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A molecular atlas of cellular vulnerability and resilience in the parkinsonian striatum. [snRNA_seq]

GSE298848 Mus musculus (mouse) Single-nucleus RNA-seq 19 samples Submitted 2026/06/01 Platform GPL30172
At a glance

Single-nucleus RNA-seq · mouse · 19 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
19 samples: 5 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.
Summary (written by the submitters)
The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinson’s disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cellular transcriptome in early and progressive PD mouse models and in human PD stages. Our analyses revealed significant transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles.
Read the full summary ↓
Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric type striatal projection neurons (SPNs) and Chst9-expressing direct pathway SPNs as the most resilient subtypes in mice and humans. This cross-species molecular atlas of the cell-state dynamics in the parkinsonian striatum uncovers the selectively vulnerable and resilient cell types that can inspire new treatment strategies.
This dataset
Open GSE298848 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 GSE298848_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1271494 and SRA study SRP589613. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly in triplicate
snRNA seq of striatum of 2 mouse models of PD… ×7 snRNA seq of striatum of 2 mouse models of PD… ×4 snRNA seq of striatum of 2 mouse models of PD… ×3 snRNA seq of striatum of 2 mouse models of PD… ×3 snRNA seq of striatum of 2 mouse models of PD… ×2

Supports a between-group comparison across 19 samples.

How we read this: 5 replicated groups read from 19 sample titles; they account for 19 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
Datasets on a similar topic

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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.