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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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

ABSTRACT: To determine whether immortalized cells derived from the rat SCN (SCN2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. This SuperSeries is composed of the following subset Series:; GSE1654: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates); GSE1673: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells: Comparison to Long-Evans Rat SCN Experiment Overall Design: Refer to individual Series

ORGANISM(S): Rattus norvegicus

SUBMITTER: Gus John Menger

PROVIDER: E-GEOD-4192 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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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Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates)

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Circadian behavior is light-reprogrammed by plastic DNA methylation

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Transcription profiling of rat immortalized SCN cells - circadian experiment

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

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

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.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).

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

RNA-seq of Mus musculus to investigate the role of RNA editing for the gene expression in the suprachiasmatic nuclei of the hypothalamus

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