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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Circadian regulation of gene expression in the SCN

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Heather Ballance

PROVIDER: E-GEOD-70392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Circadian regulation of gene expression in the SCN (gene expression)

Project description:We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq. 24 samples total covering 24 time points, with no replicates. SCN samples from mouse brains collected every 2 hours for 2 days (24 samples total).

2015-12-31 | E-GEOD-70384 | biostudies-arrayexpress

Circadian regulation of gene expression in the SCN (RNA-seq)

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2015-12-31 | E-GEOD-70391 | biostudies-arrayexpress

A circadian gene expression atlas in mammals assayed by microarray

Project description:To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional “rush hours” preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy. 288 samples total covering 12 different tissues, with no replicates. Each tissue sampled every 2 hours for 2 days (24 samples per tissue).

2014-09-30 | E-GEOD-54650 | biostudies-arrayexpress

A circadian gene expression atlas in mammals: Implications for biology and medicine

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-09-30 | E-GEOD-54652 | biostudies-arrayexpress

A circadian gene expression atlas in mammals assayed by RNA-seq

Project description:To characterize the role of the circadian clock in mouse physiology and behavior, we used RNA-seq and DNA arrays to quantify the transcriptomes of 12 mouse organs over time. We found 43% of all protein coding genes showed circadian rhythms in transcription somewhere in the body, largely in an organ-specific manner. In most organs, we noticed the expression of many oscillating genes peaked during transcriptional “rush hours” preceding dawn and dusk. Looking at the genomic landscape of rhythmic genes, we saw that they clustered together, were longer, and had more spliceforms than nonoscillating genes. Systems-level analysis revealed intricate rhythmic orchestration of gene pathways throughout the body. We also found oscillations in the expression of more than 1,000 known and novel noncoding RNAs (ncRNAs). Supporting their potential role in mediating clock function, ncRNAs conserved between mouse and human showed rhythmic expression in similar proportions as protein coding genes. Importantly, we also found that the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes. Many of these drugs have short half-lives and may benefit from timed dosage. In sum, this study highlights critical, systemic, and surprising roles of the mammalian circadian clock and provides a blueprint for advancement in chronotherapy. 96 samples total covering 12 different tissues, with no replicates. Each tissue sampled every 6 hours for 2 days (8 samples per tissue).

2014-09-30 | E-GEOD-54651 | biostudies-arrayexpress

Mouse SCN in LC-MSMS - The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

Project description:The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

2014-09-10 | PXD000778 | Pride

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Transcription profiling time series of Rattus norvegicus SCN2.2 cell line and in vivo suprachiasmatic nucleus samples to compare oscillatory properties of each transcriptome

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Identification of the circadian ubiquitylated proteome of Drosophila melanogaster.

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2018-05-22 | PXD005015 | Pride

Deep Proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice

Project description:The age and sex of studied animals profoundly impacts experimental outcomes in animal-based biomedical research. However, most preclinical studies in mice use a wide-spanning age range from 4 to 14 weeks and do not assess study parameters in male and female mice in parallel. This raises concerns regarding reproducibility and neglect of potentially relevant age and sex differences. Furthermore, the molecular setup of tissues in dependence of age and sex is unknown in naïve mice precluding efficient translational research. Here, we first compared two different mass spectrometric acquisition methods – DDA- and DIA-PASEF – in order to maximize the depth of proteome quantitation. We then employed an optimized workflow of quantitative proteomics based on DIA-PASEF followed by DIA-NN data analysis, and revealed significant differences in mouse paw skin and sciatic nerve (SCN) when comparing (i) male and female mice, and, in parallel, (ii) adolescent mice (4 weeks) with adult mice (14 weeks).

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