Transcriptomics

Dataset Information

300

Transcription profiling by high throughput sequencing of dissected tissue of the suprachiasmatic nucleus from five adult male mice


ABSTRACT: 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.

ORGANISM(S): Mus musculus  

SUBMITTER: William Pembroke   Peter L Oliver  Kay E Davies  Chris P Ponting  Arran Babbs  William G Pembroke 

PROVIDER: E-GEOD-72095 | ArrayExpress | 2015-11-03

SECONDARY ACCESSION(S): SRP062428GSE72095PRJNA292917

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Temporal transcriptomics suggest that twin-peaking genes reset the clock.

Pembroke William G WG   Babbs Arran A   Davies Kay E KE   Ponting Chris P CP   Oliver Peter L PL  

eLife 20151102


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 finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-seq over a 24 hr 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 g  ...[more]

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