Abstract
Microarray technology is at present a standardized workflow for genome-wide expression analysis. Whole-genome tiling microarrays have emerged as an important platform for flexible and comprehensive expression profiling. In this chapter we describe a detailed standardized workflow for experiments assessing the transcriptome of Arabidopsis using tiling arrays and provide useful hints for critical steps from experimental design to data analysis. Although the protocol is optimized for AGRONOMICS1 arrays, it can readily be adapted to other tiling arrays. AGRONOMICS1 is the first platform that enables strand-specific expression analysis of the Arabidopsis genome with a single array. Moreover, it includes all perfect match probes from the original ATH1 array, allowing readily integration with the large existing ATH1 knowledge base. This workflow is designed for the analysis of raw data for any number of samples and it does not pose any particular hardware requirements.
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Acknowledgments
We thank our colleagues at the Functional Genomics Center Zurich for helpful discussions. Research in the authors’ laboratories is supported by the Sixth and Seventh Framework Programs of the European Commission through the AGRON-OMICS integrated project (grant no. LSHG–CT–2006–037704) to W.G., L.H., and others and the TiMet collaborative project (grant 245143) to W.G., and by a grant from the Swedish Research Council to L.H.
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Coman, D., Gruissem, W., Hennig, L. (2013). Transcript Profiling in Arabidopsis with Genome Tiling Microarrays. In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_3
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DOI: https://doi.org/10.1007/978-1-62703-607-8_3
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