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Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer’s Disease and Primary Tauopathies

GSE327289 Homo sapiens (human) Single-nucleus RNA-seq 76 samples Submitted 2026/08/05 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 76 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
76 samples: 10 conditions, mostly in duplicateGroups 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
Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer's Disease and Primary TauopathiesResearch square · 2026
Summary (written by the submitters)
Cerebrovascular dysfunction contributes to disease progression in Alzheimer’s disease (AD) and primary tauopathies, yet molecular alterations within vascular cell populations remain poorly understood. We performed single-nucleus RNA sequencing of postmortem human inferior temporal gyrus to characterize transcriptomic changes across cerebrovascular cell types in AD and primary tauopathies, including corticobasal degeneration, Pick’s disease, and progressive supranuclear palsy.
Read the full summary ↓
Differential expression analyses revealed predominantly disease-specific transcriptional programs across vascular cell populations. However, genes involved in the heat-shock response were consistently upregulated across all diseases, suggesting a conserved cerebrovascular stress response during neurodegeneration. We also report extensive cerebrovascular remodeling taking place in AD compared with primary tauopathies and identified a dysregulation of genes within AD genome-wide association study (GWAS) loci in cerebrovascular-associated cells. Transcriptomic findings were validated using tissue clearing, light-sheet microscopy, and immunofluorescence quantification of vascular markers. We highlight shared and disease-specific vascular mechanisms in neurodegeneration with potential for newly redefined targeted therapies.
Published in
Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer's Disease and Primary Tauopathies
Estrella LD, Dasgupta S, Gundavelli A et al. · Research square 2026 · PMID 42523523 · doi:10.21203/rs.3.rs-10197270/v1
This dataset
Open GSE327289 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 GSE327289_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 PRJNA916657 and SRA study SRP415133. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42523523) ↗
Study design
10 conditions, mostly in duplicate
Vascular cells, Progressive Supranuclear Pals… ×33 Vascular cells, Alzheimer's disease, Dono ×16 Vascular cells, Pick's Disease (PiD), Dono ×8 Vascular cells, Corticobasal Degeneration (CB… ×7 Vascular cells, Control, Donor 1, ×2 Vascular cells, Control, Donor 2, ×2 Vascular cells, Control, Donor 3, ×2 Vascular cells, Control, Donor 4, ×2 +2 more

Supports a case/control comparison: 24 samples read as cases, 12 as controls.

How we read this: 10 replicated groups read from 76 sample titles; they account for 76 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

+ 36 more — browse all 76 samples with per-sample file links →

Datasets on a similar topic

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