To determine which genes are being expressed in any given cell population, mRNA molecules, which are produced by active genes as they assemble proteins, are isolated from the cells and copied with a special enzyme called "reverse transcriptase." The enzyme copies the mRNA strand by using the DNA rule (see 8), and the copy is called a cDNA. Thus, each cDNA made using reverse transcriptase corresponds directly to a specific mRNA that was coming from an active gene in the cell.

All the cDNAs are then attached to a fluorescent dye. When a DNA microarray is bathed with the fluorescent cDNAs, each cDNA molecule will bind by base-pairing to the spot where pieces of its specific matching gene are located. Therefore, each fluorescent spot in the microarray corresponds to a gene that was actively being transcribed into mRNA in the original cell.