GEO series

Septo-dentate gyrus cholinergic circuits modulate function and morphogenesis of adult neural stem cells through granule cells in mice

GSE202481 Mus musculus (mouse) Single-nucleus RNA-seq 1 samples Submitted 2024/09/04 Platform GPL21626

At a glance

Single-nucleus RNA-seq · mouse · 1 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: 1 samples
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: Septo-dentate gyrus cholinergic circuits modulate function and morphogenesis of adult neural stem cells through granule cell intermediariesProceedings of the National Academy of Sciences of the United States of America · 2024

Summary (written by the submitters)

Dentate gyrus (DG) is a critical structure for spatial memory and adult neurogenesis, and both processes are dynamically regulated by neural circuit activity. It remains unknown how neural circuits orchestrate the molecular landscape of the highly heterogeneous DG to regulate these distinct functions. Here we first report that activation of a cholinergic circuit from Diagonal Band of Broca to DG promotes both neural stem cell (NSC) activation and spatial memory.

Read the full summary ↓

Furthermore, using single-nucleus RNA-sequencing of DG, we report broad transcriptomic changes across multiple types of mature and adult-born cells in response to cholinergic circuit activation. Notably, various neuronal populations exhibit abundant molecular changes that support synaptic functions crucial for spatial memory; while NSCs exhibit molecular changes that support their structural development and neurogenic proliferation. Interestingly, our electrophysiology and NicheNet analyses reveal granule cells, endothelial cells, and astrocytes as potential intermediaries for cholinergic activity-dependent NSC regulation. Our findings provide cell-type specific molecular mechanisms underlying cholinergic circuit activity-dependent regulation of distinct DG functions.

Published in

Septo-dentate gyrus cholinergic circuits modulate function and morphogenesis of adult neural stem cells through granule cell intermediaries

Chen ZK, Quintanilla L, Su Y et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 39312657 · doi:10.1073/pnas.2405117121

This dataset

Open GSE202481 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 GSE202481_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 PRJNA836280 and SRA study SRP374191. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39312657) ↗

Samples in this study

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