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A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration [timecourse]

GSE297373 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2025/12/15 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 19 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
19 samples: 6 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
A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegenerationLife science alliance · 2026
Summary (written by the submitters)
Circadian clocks are encoded by a transcription-translation feedback loop that aligns physiological processes with the solar cycle. Previous work linking the circadian clock to the regulation of RNA-binding proteins (RBPs) provides a foundation for the vital examination of their mechanistic connections in the context of amyotrophic lateral sclerosis (ALS)—a fatal neurodegenerative disease commonly marked by disrupted RBP function.
Read the full summary ↓
Here, we reveal that the spinal cord cholinergic neuron rhythmic transcriptome is enriched for genes associated with ALS and other neurodegenerative diseases. We show that there is time-of-day-dependent expression of ALS-linked RBP transcripts and rhythmic alternative splicing of genes involved in microtubule cytoskeleton organization, intracellular trafficking, and synaptic function. Through in silico analysis of RNA sequencing data from sporadic ALS patients, we find that gene expression profiles altered in disease correspond with rhythmic gene networks. Finally, we report that clock disruption through cholinergic neuron-specific deletion of clock activator BMAL1 increases neurodegeneration and drives time-of-day-dependent alternative splicing of RNA processing genes. Our results establish a role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration.
Published in
A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration
Tam SB, Waldeck NJ, Wright M et al. · Life science alliance 2026 · PMID 41397872 · doi:10.26508/lsa.202503508
This dataset
Open GSE297373 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 GSE297373_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 PRJNA1264050 and SRA study SRP586120. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41397872) ↗
Study design
6 conditions, mostly in triplicate
WT cholinergic neurons, ZT0, biol ×3 WT cholinergic neurons, ZT4, biol ×3 WT cholinergic neurons, ZT8, biol ×3 WT cholinergic neurons, ZT12, biol ×3 WT cholinergic neurons, ZT16, biol ×3 WT cholinergic neurons, ZT20, biol ×3 WT cholinergic neurons, pooled input ×1

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 19 sample titles; they account for 18 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
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