The ability to track changes in the levels of many metabolites in plants has great utility in a number of biological contexts. A metabolomics experiment usually requires the comparison of different varieties in either a functional genomics context or in response to perturbation by an external treatment. Such treatments can result in subtle changes in the final chemical signature of the plant tissue, and therefore, any unwanted variance produced in the generation of that tissue must be minimised. Procedures for plant growth, harvesting, preparation of extracts, and the subsequent collection of data have been optimised to minimise experimental variation within the dataset. This chapter describes in detail how to generate reproducible Arabidopsis tissue suitable for a typical plant metabolomics experiment. Issues concerned with tissue sampling, harvesting, and storage are also discussed.
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