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Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker.

Nucleic acids research | Sep 29, 2017

The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. A total of 79 microarrays were used (24 SCN and 55 WB samples, 4 different microarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB). 31 684 MGI gene symbols had data for at least one platform. Meta-analysis using a random effects model for weighting individual effect sizes (derived from differential expression between relevant SCN and WB samples) reliably detected known SCN markers. SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers.

Pubmed ID: 28973476 RIS Download

Mesh terms: Animals | Brain Chemistry | Circadian Clocks | Circadian Rhythm | Data Mining | Datasets as Topic | Gene Ontology | Gene Regulatory Networks | Male | Mice | Mice, Inbred C57BL | Molecular Sequence Annotation | Oligonucleotide Array Sequence Analysis | Sequence Analysis, RNA | Suprachiasmatic Nucleus | Transcriptome

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GENSAT

Publicly available gene expression atlas of the developing and adult central nervous system in the mouse, using both in situ hybridization and transgenic mouse techniques. It is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse. Using EGFP BAC-transgenics, this project provides the scientific community with tools to catalog, map, and electrophysiologically record from individual cells. The application of Cre recombinase technologies allows for cell-specific gene manipulation. The transgenic mice created by this project are available to the scientific community.

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