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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.Â 8 samples total covering 8 time points, with no replicates. SCN samples from mouse brains collected every 6 hours for 2 days (8 samples total).

ORGANISM(S): Mus musculus

SUBMITTER: Heather Ballance

PROVIDER: E-GEOD-70391 | 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

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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

Circadian regulation of gene expression in the SCN

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

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

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SCN lightpulse timecourse

Project description:The aim of the experiment was to identify genes in the mouse suprachiasmatic nucleus whose expression was altered by exposure to a light pulse of 400 lux at CT16 (subjective night). C57BL/6 male mice were entrained to a 12:12 LD cycle and given a 30 min 400 lux light pulse at CT16. Punches of SCN tissue were collected at 30 (LP30), 60 (LP60)and 120 (LP120) mins after the start of the light pulse and flash frozen on dry ice. Sham SCN punches (Sham) were collected from mice not exposed to light at CT16. Total RNA from individual tissue samples was extracted using RNeasy micro kit from Qiagen using the lipid tissue protocol according to manufacturer's recommendations. Individual samples were analyzed for quality using an Agilent Bioanalzyer and only samples with a RIN of 8 and above were used. Samples were quantified by Nanodrop and 300ug of total RNA was used to prepare probes for hybridisation to Affymetrix Mouse Exon arrays. Probe preparation and array hybridisation was carried out according to Affymetrix protocols. Each array represents an individual SCN tissue punch.<br><br>

2013-12-16 | E-MEXP-3933 | biostudies-arrayexpress

Circadian behavior is light-reprogrammed by plastic DNA methylation

Project description:The timing of daily M-bM-^@M-^\circadianM-bM-^@M-^] behavior can be highly variable among different individuals, and twin studies suggest that about half of this variability is environmentally controlled. Similar plasticity can be seen in mice exposed to an altered lighting environment M-bM-^@M-^S for example, 22-hour days instead of 24-hour ones M-bM-^@M-^S which stably alters the genetically determined period of circadian behavior for months. The mechanisms mediating these environmental influences are unknown. Here, we show that transient exposure of mice to such lighting stably alters global transcription in the suprachiasmatic nucleus of the hypothalamus (the SCN, the M-bM-^@M-^\master clockM-bM-^@M-^] tissue determining circadian behavior in mammals). We have also showed that, these changes in transcription are due to change in DNA methylation in the SCN. Indeed, genome-wide methylation profiling revealed global alterations in promoter DNA methylation in the SCN. Importantly, infusion of a methyltransferase inhibitor to the SCN during 22-hour days suppressed period changes. We also found that these behavioral and DNA methylation changes are reversible upon entrainment to 24-hours days. We conclude that the SCN utilizes DNA methylation as a mechanism to drive circadian clock plasticity. MeDIP array of profiling, demonstrated that genomicDNA methylation changes in mice entrained to short-T cycle. comparison of methylation profile in the suprachiasmatic nuclei of mice entrained to normal T-cycle and short T-cycle

2014-01-14 | E-GEOD-54021 | biostudies-arrayexpress

Transcription profiling of mouse SCN after 30-min light pulse

Project description:The transmission of information about the photic environment to the circadian clock involves a complex array of neurotransmitters, receptors, and second messenger systems. Using laser capture microscopy and microarray analysis, a population of genes rapidly induced by light in the suprachiasmatic nucleus is identified. Experiment Overall Design: Mice were exposed starting at 1 hour after lights off to a 30-minute light pulse. At the end of the light pulse, mice were euthanized and the brains extracted. Cells from the suprachiasmatic nucleus were extracted using laser capture microscopy and gene expression was quantified using Affymetrix microarrays. Genes showing a significant increase in expression following the light pulse as compared to a sham light pulse were identified.

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RNA-seq of neuronal SOX2-ablated murine suprachiasmatic nuclei against wild-type littermate controls

Project description:Mice lacking the stem/progenitor cell transcription factor, Sex determining region Y-box 2 (SOX2), in neurons of the suprachiasmatic nuclei display imprecise, poorly consolidated behavioral rhythms that do not entrain efficiently to environmental light cycles. RNA sequencing revealed that Sox2 deficiency alters the circadian transcriptome of the SCN, reducing the expression of many core clock genes and neuropeptide-receptor systems.

2019-03-18 | E-MTAB-7496 | biostudies-arrayexpress

Temporal transcriptomics suggest that twin-peaking genes reset the clock

Project description:The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the true nature of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-Seq over a 24-hour light / dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase-shifting of the circadian clock. 342 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms. Pooled dissected tissue of the suprachiasmatic nucleus from five adult male mice provided one of three replicates for each of six time points over a 12:12 light/dark (LD) cycle (ZT2, 6, 10, 14, 18 and 22). Each biological replicate was sequenced over 3 separate lanes using Illumina HiSeq.

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