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Human microglia differentially respond to ß-amyloid, tau, and combined Alzheimer's disease pathologies in vivo

GSE311382 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2025/11/29 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 16 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
16 samples: 4 × control, vs 4 × Interferon alpha, vs 4 × Interferon beta, vs 4 × Interferon gamma,Groups 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
Human microglia differentially respond to β-amyloid, tau, and combined Alzheimer's disease pathologies in vivoAlzheimer's & dementia : the journal of the Alzheimer's Association · 2025
Summary (written by the submitters)
Recent studies have identified important species-dependent differences in the response of microglia to beta-amyloid pathology. Yet, whether human microglia also interact differently with the pathognomonic combination of amyloid and tau pathologies that occurs in Alzheimer’s Disease (AD) remains unclear. We generated a xenotolerant mouse model of AD that develops both plaque and tangle pathologies, transplanted stem cell derived microglial progenitors and examined the interactions between human microglia and AD pathologies with scRNA sequencing, immunohistochemistry, and in vitro modeling.
Read the full summary ↓
Combined amyloid and tau pathologies induced robust type-I interferon and proinflammatory cytokine responses, as well as an increased adoption of a distinct “rod” morphology in human microglia. The Rod morphology could be induced with type-I interferon treatment in vitro. We provide new insights into human microglial responses to combined AD pathologies and a novel platform to investigate and manipulate human microglia in vivo.
Published in
Human microglia differentially respond to β-amyloid, tau, and combined Alzheimer's disease pathologies in vivo
Coburn MA, Eskandari-Sedighi G, Hasselmann J et al. · Alzheimer's & dementia : the journal of the Alzheimer's Association 2025 · PMID 41268790 · doi:10.1002/alz.70930
This dataset
Open GSE311382 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 GSE311382_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 PRJNA1369384 and SRA study SRP648832. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41268790) ↗
Study design
4 × control, vs 4 × Interferon alpha, vs 4 × Interferon beta, vs 4 × Interferon gamma,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.