GEO series

The spatial landscape of glial pathology and T-cell response in Parkinson’s disease substantia nigra [snRNAseq]

GSE253462 Homo sapiens (human) Single-nucleus RNA-seq 41 samples Submitted 2025/07/09 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 41 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: Homo sapiens (human)
Samples: 41 samples: 41 samples, each with a distinct title — no replicated groupsGroups 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: The spatial landscape of glial pathology and T cell response in Parkinson's disease substantia nigraNature communications · 2025

Summary (written by the submitters)

Recent evidence, including identification of specific peripheral T-cell receptor sequences, indicates the adaptive immune response is associated with disease pathogenesis. However, the properties of T-cells in the brain regions where neurons degenerate are uncharacterized. We have analyzed the identities and interactions of T-cells in PD in post-mortem brain tissue using single nucleus RNA sequencing, spatial transcriptomics and T-cell receptor sequencing.

Read the full summary ↓

We found that T-cells in the substantia nigra of PD brain donors exhibit a CD8+ resident memory phenotype, increased clonal expansion, and altered spatial relationships with astrocytes, myeloid cells, and endothelial cells. We also describe regional differences in astrocytic responses to neurodegeneration. Our findings nominate potential molecular and cellular candidates that allow a deeper understanding of the pathophysiology of neurodegeneration in PD. Together, our work represents a major single nucleus and spatial transcriptional resource for the fields of neurodegeneration and PD

Published in

The spatial landscape of glial pathology and T cell response in Parkinson's disease substantia nigra

Ma M, Paryani F, Jakubiak K et al. · Nature communications 2025 · PMID 40759663 · doi:10.1038/s41467-025-62478-3

This dataset

Open GSE253462 in finder → Find more human 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 GSE253462_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 PRJNA1065855 and SRA study SRP484254. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40759663) ↗

Study design

41 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 41 sample titles: 41 distinct titles with little repetition. 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

GSM8021001 T-362, snRNA
GSM8021002 T-343, snRNA
GSM8021003 T-257, snRNA
GSM8021004 T-551, snRNA
GSM8021005 T-290, snRNA
GSM8021006 T-1619, snRNA
GSM8021007 T-777, snRNA
GSM8021008 T-1952, snRNA
GSM8021009 T-308, snRNA
GSM8021010 T-2017, snRNA
GSM8021011 T-1976, snRNA
GSM8021012 T-233, snRNA
GSM8021013 T-4162, snRNA
GSM8021014 T-3860, snRNA
GSM8021015 T-4174, snRNA
GSM8021016 T-4462, snRNA
GSM8021017 T-3998, snRNA
GSM8021018 T-4857, snRNA
GSM8021019 T-4815, snRNA
GSM8021020 T-4235, snRNA
GSM8021021 T-4515, snRNA
GSM8021022 T-0081, snRNA
GSM8021023 T-4934, snRNA
GSM8021024 T-2791, snRNA
GSM8021025 T-5498, snRNA
GSM8021026 T-4938, snRNA
GSM8021027 T-2007, snRNA
GSM8021028 T-4839, snRNA
GSM8021029 T-4116, snRNA
GSM8021030 T-5359, snRNA
GSM8021031 T-5547, snRNA
GSM8021032 T-5227, snRNA
GSM8021033 T-5133, snRNA
GSM8021034 T-4424, snRNA
GSM8021035 T-3799, snRNA
GSM8021036 OJ5, snRNA
GSM8021037 T-5385, snRNA
GSM8021038 T-5259, snRNA
GSM8021039 T-4530, snRNA
GSM8021040 T-2465, snRNA

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

GSE329625 A deep cellular atlas of the human ventral substantia nigra in Parkinson's identifies a genetic and molecular overlap with insulin resistance 20 samples shares substantia, parkinson, nigra
GSE281069 Mapping the glial transcriptome in Huntington’s disease using snRNAseq: Selective disruption of glial signatures across brain regions 44 samples shares snrnaseq, glial
GSE273787 Pathways underlying selective neuronal vulnerability in Alzheimer's disease: contrasting the vulnerable locus coeruleus to the resilient substantia nigra 44 samples shares substantia, nigra
GSE253569 Molecular Insights into PCB Neurotoxicity: Comparing Transcriptomic Responses across Dopaminergic Neurons, Population Blood Cells, and Parkinson's Disease Pathology 24 samples shares pathology, parkinson
GSE272394 Inflammatory intracellular signaling in neurons is influenced by glial soluble factors in iPSC-based cell model of PARK2-associated Parkinson’s disease 16 samples shares parkinson, glial
GSE333851 Spatial Glyco-Codes Define Human Liver Pathology and Progression 32 samples shares pathology, spatial
GSE320389 Attention-based deep learning for analysis of pathology images and gene expression data in lung squamous premalignant lesions 215 samples shares pathology
GSE320381 Attention-based deep learning for analysis of pathology images and gene expression data in lung squamous premalignant lesions [HTAN cohort] 145 samples shares pathology

Search all human 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.