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Molecular signatures and spatial distribution of disease-associated cellular populations in early-onset Alzheimer's disease mouse brain

GSE253570 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/06/20 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 12 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
Mus musculus (mouse)
Samples
12 samples: 3 × mouse, WT, snRNA-seq, vs 3 × mouse, 5×FAD, snRNA-seq,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.
Summary (written by the submitters)
Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder. Grasping the pathological transformations in early-phase AD is important. Integrating single-cell and spatial transcriptomics with the pathophysiology of AD from the same origin permits to delineate molecular characteristics and spatial arrangement of cellular populations without individual differences, however, such experimental designs have been ignored in current studies.
Read the full summary ↓
Here, we use a single-source experimental framework to create a multimodal dataset of disease-susceptible region in early-onset Alzheimer's Disease (EOAD) mouse. Predicated on amyloid-beta (Aβ) immunopathology, a profile of disease-associated alterations is discerned. Mature myelinating oligodendrocytes within fiber tracts exhibit compromised fatty acid synthesis and energy-related processes. Region-specific glutamatergic neurons demonstrate impaired synaptic formation, coupled with transcriptomic modifications that encompass energy homeostasis, lipid metabolism and cellular adhesion. Disease-associated astrocytes, aggregating around Aβ deposits, exhibit neuron-related changes in oxidative phosphorylation (OxPhos) and metal ion responses. This investigation serves as a resource for exploring disease signature across multimodal, which provides a basis for finding the progression mechanisms of AD.
This dataset
Open GSE253570 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 GSE253570_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 PRJNA1066303 and SRA study SRP484648. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × mouse, WT, snRNA-seq, vs 3 × mouse, 5×FAD, snRNA-seq,

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 6 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

Search all mouse 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.