Seeds provide much of the economic value in agricultural products, and numerous research efforts are aimed toward understanding the regulation of the storage compound accumulation in crop seeds. With its fully sequenced genome, Arabidopsis thaliana (thale cress) has now become the dominant model system in dicot plant science, including seed biology. Unfortunately, Arabidopsis seeds are very small and not always amendable to study. For example, the application of microarray technology to large-scale gene expression profiling in Arabidopsis seeds can be limited because of the relatively large amount of RNA needed to prepare probes. Another potentially restrictive factor is that seeds are difficult material for RNA isolation because of high amounts of secondary metabolites and polysaccharides. In our experience, commercial kits and widespread plant RNA extraction methods are unsatisfactory in preparing microarray probes using Arabidopsis or other seeds. Here, we describe a rigorous procedure that enabled us to isolate high-quality RNA and perform successful microarray experiments using small amounts of developing Arabidopsis seeds.
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