Global Profiling of the Circadian Transcriptome Using Microarrays

  • Polly Yingshan Hsu
  • Stacey L. HarmerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1158)


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.

Key words

Transcriptome Microarray Circadian rhythms Cycling genes JTK_CYCLE 



We thank Hsin-Yen Wu for reading and testing the commands in this manuscript, and Michael Hughes for helpful discussions about JTK_CYCLE. This work was supported by the National Institutes of Health (NIGMS) ( [GM069418] and the Taiwan Merit Scholarship ( [NSC-095-SAF-I-564-014-TMS].


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Plant BiologyUniversity of CaliforniaDavisUSA

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