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Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points

GSE261596 Mus musculus (mouse) Single-nucleus RNA-seq 12 samples Submitted 2025/02/24 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 12 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). 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: 12 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
Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time pointsJournal of cell communication and signaling · 2025
Summary (written by the submitters)
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease and the most common form of dementia. AD is characterized by progressive memory loss and cognitive decline, affecting behavior, speech, and motor abilities. The neuropathology of AD includes the formation of extracellular amyloid-β plaques and intracellular neurofibrillary tangles of phosphorylated tau, as well as neuronal loss.
Read the full summary ↓
Although neuronal loss is a primary hallmark of AD, non-neuronal cell populations are known to maintain brain homeostasis and neuronal health through neuron-glia and glial cell crosstalk via chemical messengers. To investigate altered glia-neuron communication in the presence of amyloid-β and tau pathology, we generated snRNA-seq data from the hippocampus of 3xTg-AD mice at 6 and 12 months and age-matched wild-type littermates. We predicted altered glia-neuron interactions between senders (astrocytes, microglia, oligodendrocytes, and OPCs) and receivers (excitatory and inhibitory neurons) across time points. We further investigated these interactions through pseudo-bulk differential expression, functional enrichment, and gene regulatory analyses.
Published in
Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points
Soelter TM, Howton TC, Wilk EJ et al. · Journal of cell communication and signaling 2025 · PMID 40026671 · doi:10.1002/ccs3.70006
This dataset
Open GSE261596 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 GSE261596_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 PRJNA1088080 and SRA study SRP495269. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40026671) ↗
Study design
12 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 12 sample titles: 12 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
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.