Functional genomic analysis in pain research using hybridization arrays

Hybridization array technology makes it possible to compare global gene-expression patterns in any experimental context for which good-quality RNA can be generated. To date, DNA arrays have been used as a tool to compare functional genomic changes (differences in wholesale gene expression) in studies that cover an impressive variety of research disciplines including cancer, yeast genomics, and, more recently, neuroscience and behavior. The basic premise of the array experiment is that one interrogates a panel of probes (gene-specific cDNA fragments or gene-specific oligonucleotides that have been immobilized on a solid support) with RNAs (targets) from control and treated experimental samples that have been either radioactively or fluorescently labeled. Signal derived from either competitive (both samples on a single chip) or differential (one sample/one chip) hybridization is used to calculate relative gene expression. There are three widely used platforms available to perform array experiments (Affymetrix GeneChips, oligonucleotide arrays, and membrane-based cDNA arrays) and each platform offers advantages and limitations. The experimental description in this chapter explains, in detail, how to perform a hybridization array using the macroarray platform.