All microarray techniques use a solid support, such as a glass slide, onto which DNA sequences that are representative of single genes of a given species are spotted that are representative of single genes of a given species. Such arrays can hold thousands of spots, which can all be investigated together in a single experiment, greatly increasing the throughput of gene analysis over the classic methods mentioned in the text. RNA extracted from a given tissue is first transformed by reverse transcription into a more stable DNA copy (a cDNA) of each RNA molecule represented in the extract (Web Figure 2.4.A). The cDNA mixture is then labeled with a fluorescent dye to allow its visualization later in the procedure. After labeling, the cDNA mixture is applied to the microarray.

Each single-stranded cDNA binds to (hybridizes with) its corresponding (complementary) DNA spot on the microarray, which represents the gene that produced the corresponding mRNA in the original tissue extract. For example, if mRNA from gene X is present in the tissue extract, its cDNA will bind to the spot on the microarray that represents gene X. If gene Y, however, was not expressed at the time of tissue sampling, there will be no cDNA to bind to the DNA spot on the microarray that represents gene Y, and that spot will stay blank. After hybridization, the microarray is scanned using a laser beam that can detect the fluorescent label applied to the cDNA. In our example, the spot for gene X will light up in the laser scan, whereas the spot for gene Y will not.

There are several types of microarray techniques. While some types analyze two mRNA samples—for example, from a treated plant and a control plant—on a single microarray (using "two-color labeling"; see Web Figure 2.4.A), other types compare two samples using two separate microarrays. Since its original application to the analysis of gene expression, microarray technology has been adapted to many other uses as well, ranging from diagnosing the genotypes of individuals in a population to determining the epigenetic status of genes or intergenic regions.

Web Figure 2.4.A  Two-color labeling is a microarray technique that can be used to compare gene expression in different individuals or under different conditions.