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| Status |
Public on May 02, 2024 |
| Title |
Characterisation of the epidermal diurnal transcriptome of mice with tissue-specific circadian clock activity [LD] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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. 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.
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| Overall design |
The diurnal transcriptome of the skin epidermis was profiled for mice in which circadian clock activity was present only in the skin epidermis, only in the brain, only in the skin and brain, or all tissues. Profiling was undertaken by performing RNA-seq of epidermis samples taken at four hour intervals throughout the day (four biological replicates per timepoint), and subsequently the algorithms JTK_CYCLE and BIOCYCLE were used to generate a consensus diurnal transcriptome for each condition. In addition, the algorithm DryR was used to identify groups of genes with specific rhythmic parameters either shared or differing between the different conditions.
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| Contributor(s) |
Mortimer T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 02, 2021 |
| Last update date |
May 02, 2024 |
| Contact name |
Thomas Mortimer |
| E-mail(s) |
thomas.mortimer@irbbarcelona.org
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| Organization name |
IRB Barcelona
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| Street address |
Carrer Baldiri Reixac 10-12
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| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (96)
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| This SubSeries is part of SuperSeries: |
| GSE190035 |
Characterisation of the epidermal diurnal and circadian transcriptomes of mice with tissue-specific circadian clock activity |
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| Relations |
| BioProject |
PRJNA785616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190032_BIOCYCLE_BrainRE_LD.tsv.gz |
3.1 Mb |
(ftp)(http) |
TSV |
| GSE190032_BIOCYCLE_EpiRE_LD.tsv.gz |
3.0 Mb |
(ftp)(http) |
TSV |
| GSE190032_BIOCYCLE_RERE_LD.tsv.gz |
3.3 Mb |
(ftp)(http) |
TSV |
| GSE190032_BIOCYCLE_WT_LD.tsv.gz |
3.3 Mb |
(ftp)(http) |
TSV |
| GSE190032_JTK_BrainRE.RNAseq_LD.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE190032_JTK_EpiRE.RNAseq_LD.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE190032_JTK_RERE.RNAseq_LD.txt.gz |
3.7 Mb |
(ftp)(http) |
TXT |
| GSE190032_JTK_WT.RNAseq_LD.txt.gz |
3.8 Mb |
(ftp)(http) |
TXT |
| GSE190032_dryR_results_LD.xlsx |
24.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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