GEO series

Distinct molecular mechanisms of stress habituation in the mouse hippocampus [snRNA-seq]

GSE292239 Mus musculus (mouse) Single-nucleus RNA-seq 23 samples Submitted 2025/03/18 Platform GPL34328

At a glance

Single-nucleus RNA-seq · mouse · 23 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: Mus musculus (mouse)
Samples: 23 samples: 8 conditions, mostly in triplicateGroups 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: Distinct mechanisms of transcriptomic habituation to repeated stress in the mouse hippocampusNature communications · 2025

Summary (written by the submitters)

We explore how the tightly regulated molecular response triggered by acute restraint stress becomes altered after repeated restraint exposure. Transcriptomic sampling of the mouse hippocampus at multiple time points revealed that repeated stress leads to widespread habituation, damping stress-induced gene expression of all stress-responsive genes.

Read the full summary ↓

However, we find no evidence for the emergence of new response profiles or alterations in baseline gene expression. Using single-cell multi-omics, we show that these findings hold true across cell types, and we reveal cell type specific patterns of habituation. Transcriptomic and chromatin accessibility profiles identify two distinct mechanisms that contribute to the observed habituation patterns: an early cAMP-associated mechanism that is related to blunted transcription after chronic stress, and a late corticosterone-dependent mechanism that is linked to a shortened transcriptional response.

Published in

Distinct mechanisms of transcriptomic habituation to repeated stress in the mouse hippocampus

Waag R, von Ziegler L, Sonder E et al. · Nature communications 2025 · PMID 41430076 · doi:10.1038/s41467-025-67825-y

This dataset

Open GSE292239 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 GSE292239_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 PRJNA1237719 and SRA study SRP571283. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41430076) ↗

Study design

8 conditions, mostly in triplicate

scRNA, Restraint_15min_S ×3 scRNA, Handling_Control_S ×3 scRNA, Restraint_3h_S ×3 scRNA, Handling_3h_S ×3 scRNA, Restraint_45min_S ×3 scRNA, Restraint_Control_S ×3 scRNA, Handling_15min_S ×3 scRNA, Handling_45min_S ×2

Supports a between-group comparison across 23 samples.

How we read this: 8 replicated groups read from 23 sample titles; they account for 23 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

GSM8853934 scRNA, Restraint_15min_S1 scRNA, Restraint_15min_S
GSM8853935 scRNA, Handling_Control_S10 scRNA, Handling_Control…
GSM8853936 scRNA, Restraint_3h_S11 scRNA, Restraint_3h_S
GSM8853937 scRNA, Handling_45min_S12 scRNA, Handling_45min_S
GSM8853938 scRNA, Restraint_15min_S13 scRNA, Restraint_15min_S
GSM8853939 scRNA, Handling_3h_S14 scRNA, Handling_3h_S
GSM8853940 scRNA, Restraint_45min_S15 scRNA, Restraint_45min_S
GSM8853941 scRNA, Restraint_Control_S16 scRNA, Restraint_Contro…
GSM8853942 scRNA, Restraint_3h_S17 scRNA, Restraint_3h_S
GSM8853943 scRNA, Handling_3h_S18 scRNA, Handling_3h_S
GSM8853944 scRNA, Handling_Control_S19 scRNA, Handling_Control…
GSM8853945 scRNA, Restraint_45min_S20 scRNA, Restraint_45min_S
GSM8853946 scRNA, Restraint_15min_S21 scRNA, Restraint_15min_S
GSM8853947 scRNA, Restraint_Control_S22 scRNA, Restraint_Contro…
GSM8853948 scRNA, Handling_15min_S23 scRNA, Handling_15min_S
GSM8853949 scRNA, Handling_45min_S24 scRNA, Handling_45min_S
GSM8853950 scRNA, Restraint_Control_S3 scRNA, Restraint_Contro…
GSM8853951 scRNA, Handling_15min_S4 scRNA, Handling_15min_S
GSM8853952 scRNA, Restraint_45min_S5 scRNA, Restraint_45min_S
GSM8853953 scRNA, Handling_3h_S6 scRNA, Handling_3h_S
GSM8853954 scRNA, Handling_Control_S7 scRNA, Handling_Control…
GSM8853955 scRNA, Restraint_3h_S8 scRNA, Restraint_3h_S
GSM8853956 scRNA, Handling_15min_S9 scRNA, Handling_15min_S

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