GEO series

Characterisation of the epidermal diurnal transcriptome of mice with K14-Cre-driven Bmal1 knockout

GSE255474 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/05/02 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples
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 GSE255474 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 GSE255474_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 PRJNA1075084 and SRA study SRP489146. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38701785) ↗

Samples in this study

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+ 24 more — browse all 24 samples with per-sample file links →

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GSE232957 Muscle-specific rescue of Bmal1 impacts survival and health span of the Bmal1-KO mouse 72 samples shares bmal1
GSE253735 Loss of skeletal muscle Bmal1 +/- Exercise Training [Mouse liver, heart, inguinal white adipose and lung tissues 64 samples shares bmal1
GSE294336 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Aged_adult] 48 samples shares bmal1
GSE294339 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Col14] 48 samples shares bmal1
GSE255357 Pharmacological Modulation of BMAL1 Alters Circadian Dynamics and the Macrophage Immune Response 36 samples shares bmal1
GSE279310 The circadian clock gene BMAL1 modulates autoimmunity features in lupus 20 samples shares bmal1

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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.