Target Preparation for DNA Microarray Hybridization

DNA microarrays are widely used to analyze genome-wide gene expression patterns and to study genotypic variations. They are miniaturized collections of thousands of DNA fragments arrayed on a surface. Based on nucleic acid complementary binding, they serve as a tool to interrogate complex populations of nucleic acids for abundance or binding affinity of particular sequences. Before a nucleic acid (target) can be used for hybridization to the probes of a microarray, it needs to be extracted from the tissue and labeled. Frequently, it also needs to be amplified to increase detection sensitivity. During a hybridization process, labeled target molecules with sequences complementary to the probes are captured quantitatively. Subsequently, a reader measures the amount of label on each probe. To generate accurate and informative data, one of the most critical aspects of these experiments is the quality of both the isolated and the labeled nucleic acid samples. This chapter describes detailed procedures for the preparation of labeled RNA samples for DNA microarray analysis.