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Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the murine cortex

GSE237419 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2024/08/19 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 10 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
10 samples: 5 × Wildtype homecage control harvested at ZT hour 7, vs 5 × Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep,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
Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortexbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Sleep loss regulates gene expression throughout the brain and impacts learning and memory. However, the molecular consequences of sleep deprivation and the ability of subsequent sleep (recovery sleep) to restore baseline gene expression remain underexplored. Our goal here is to overview transcriptional changes at the gene level in the cortex of adult male wildtype mice in response to sleep loss and recovery sleep.
Read the full summary ↓
This dataset constitutes an integration of novel data with two publicly available RNA-seq studies and contains 3, 5, and 6 hours of sleep deprivation and 2 and 6 hours of recovery sleep time points.
Published in
Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex
Popescu A, Ottaway C, Ford K et al. · bioRxiv : the preprint server for biology 2024 · PMID 39229182 · doi:10.1101/2024.08.20.607983
This dataset
Open GSE237419 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 GSE237419_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA994922 and SRA study SRP449604. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39229182) ↗
Study design
5 × Wildtype homecage control harvested at ZT hour 7, vs 5 × Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep,

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.