title: Global profiling of the circadian transcriptome using microarrays.
abstract: Circadian rhythms are biological cycles with a period length of approximately 24 h that are generated by endogenous clocks. The application of microarrays for high-throughput transcriptome analysis has led to the insight that substantial portions of the transcriptomes of both humans and many model organisms are clock-regulated. In a typical circadian time course microarray experiment, samples are collected from organisms maintained in constant environmental conditions, gene expression at each time point is determined using microarrays, and finally clock-regulated transcripts are identified using statistical algorithms. Here, we describe how to design the experiment, process RNA, determine expression profiles using ATH1 microarrays, and use a nonparametric statistical algorithm named JTK_CYCLE in order to identify circadian-regulated transcripts in Arabidopsis. This basic procedure can be modified to identify clock-regulated transcripts in different organisms or using different expression analysis platforms.
authors.affiliation: Department of Plant Biology, University of California, Davis, CA, USA.
authors.forename: Polly Yingshan
authors.initials: PY
authors.lastname: Hsu
authors.forename: Stacey L
authors.initials: SL
authors.lastname: Harmer
mesh_terms: D000465:Algorithms; D057906:Circadian Clocks / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D059467:Transcriptome