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Characterisation of the epidermal diurnal transcriptome of mice with tissue-specific circadian clock activity [LD]

GSE190032 Mus musculus (mouse) RNA-seq (gene expression) 96 samples Submitted 2024/05/02 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 96 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
96 samples: 24 conditions, mostly with about 4 replicates eachGroups 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
The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasisCell stem cell · 2024
Summary (written by the submitters)
To preserve a state of health, mammals employ an integrated network of molecular oscillators to drive daily rhythms of tissue-specific homeostatic processes. Importantly, the output, structure and coherence of this network is compromised by physiological ageing, disease and lifestyle changes. Yet, the key signalling nodes in this network, their underlying mechanisms of communication, and potential for therapeutic intervention, remain undefined.
Read the full summary ↓
To dissect this system, we construct a minimal clock network consisting of two communicating nodes: the peripheral epidermal clock and central brain clock. We show that communication between the brain and epidermal clocks is sufficient for wild-type core clock activity and specific homeostatic processes, but inputs from other clock nodes are essential for full daily physiology. Unexpectedly, we find evidence that the epidermal clock selectively suppresses or interprets systemic signals to ensure coherence of specific homeostatic processes, identifying an unrecognised gatekeeper role for peripheral clocks. Together, we introduce a novel approach for dissecting a tissues daily physiology, and in turn identify key signalling nodes required to maintain epidermal homeostasis.
Published in
The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis
Mortimer T, Zinna VM, Atalay M et al. · Cell stem cell 2024 · PMID 38701785 · doi:10.1016/j.stem.2024.04.013
This dataset
Open GSE190032 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 GSE190032_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 PRJNA785616 and SRA study SRP352132. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38701785) ↗
Study design
24 conditions, mostly with about 4 replicates each
EpiRE_ZT0 ×4 EpiRE_ZT4 ×4 EpiRE_ZT8 ×4 EpiRE_ZT12 ×4 EpiRE_ZT16 ×4 EpiRE_ZT20 ×4 BRE_ZT0 ×4 BRE_ZT4 ×4 +16 more

Supports a between-group comparison across 96 samples.

How we read this: 24 replicated groups read from 96 sample titles; they account for 96 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

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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