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mTOR signaling contributes to system-driven rhythmic gene expression in mouse liver

GSE301899 Mus musculus (mouse) RNA-seq (gene expression) 282 samples Submitted 2026/05/07 Platform GPL30172Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 282 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
282 samples: 90 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.
Summary (written by the submitters)
Rhythmic gene expression is essential to the temporal organization of biological processes across the day. While this rhythmicity is regulated by the circadian clock present in nearly every cell, accumulating evidence indicates that cycling transcriptomes are also controlled by rhythmic systemic signals that originate from the daily rhythm of food intake and that bypass peripheral clocks to initiate rhythmic transcription.
Read the full summary ↓
The underlying mechanisms remain however largely unknown. Here, we show that signaling through the nutrient-sensing kinase mTOR is both necessary and sufficient to mediate food intake-driven rhythmic gene expression in mouse liver. Pharmacological inhibition of mTOR just before the active phase desynchronizes the phase of mTOR-driven rhythmic genes without affecting clock-controlled rhythmic genes. Importantly, clock-driven and mTOR-driven genes regulate similar biological pathways, suggesting that desynchronization between clock and systemic signals, such as in shift workers, contributes to desynchronized rhythms in gene expression and consequently to disease. Our findings also suggest that using mTOR inhibitors to re-synchronize rhythms driven by systemic signals may help alleviate circadian rhythm disorders.
This dataset
Open GSE301899 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 GSE301899_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 PRJNA1287702 and SRA study SRP599308. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
90 conditions, mostly in triplicate
WT_NF_TM_ZT04 ×4 WT_NF_TM_ZT10 ×4 WT_NF_TM_ZT16 ×4 WT_NF_TM_ZT22 ×4 WT_AF_TM_ZT04 ×4 WT_AF_TM_ZT10 ×4 WT_AF_TM_ZT16 ×4 WT_AF_TM_ZT22 ×4 +82 more

Supports a between-group comparison across 282 samples.

How we read this: 90 replicated groups read from 282 sample titles; they account for 282 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

+ 242 more — browse all 282 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.