Global Profiling of the Circadian Transcriptome Using Microarrays
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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 wordsTranscriptome 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) (http://www.nigms.nih.gov/) [GM069418] and the Taiwan Merit Scholarship (http://web1.nsc.gov.tw/) [NSC-095-SAF-I-564-014-TMS].
- 12.NanoDrop, Technologies, Inc. (2007) ND-1000 Spectrophotometer User’s ManualGoogle Scholar
- 13.Dalgaard P (2009) Introductory statistics with R. Springer, New YorkGoogle Scholar
- 14.Adler J (2010) R in a Nutshell. O’Reilly Media, Sebastopol, CAGoogle Scholar
- 18.Irizarry RA, Gautier L, Huber W, Bolstad B (2006) makecdfenv: CDF environment maker. R package version 1360Google Scholar
- 19.Gohlmann H, Talloen W (2010) Gene expression studies using Affymetrix microarrays. CRC Press, Boca Raton, FLGoogle Scholar