Principle of cDNA microarray assay of gene expression

          A microarray is a set of short Expressed Sequence Tags (ESTs) made from a cDNA library of a set of known (or partially known) gene loci. The ESTs are spotted onto a cover-slip-sized glass plate, shown here as a 8x12 array. Microarrays with many thousand ESTs are now routine.

          A complete set of mRNA transcripts (the transcriptome) is prepared from the tissue of an experimental treatment or condition, e.g. fish fed a high-protein diet, or an individual with breast cancer. Complementary DNA (cDNA) reverse transcripts are prepared and labelled with a [red] fluorescent dye. A control library is constructed from an untreated source, e.g. a standard fish diet, or non-cancerous breast tissue; this library is labelled with a different fluorescent [green] dye. The experimental and control libraries are hybridized to the microarray.  A Dual-Channel Laser excites the corresponding dye, and the fluorescence intensity indicates the degree of hybridization that has occurred. Relative gene expression is measured as the ratio of the two fluorescence wavelengths. Increased expression of genes ("up-regulation") in the experimental transcriptome relative to the control is visualized as a "hot" red "pseudo-color." Decreased expression ("down-regulation") shows as a "cool" green. Intensity of either color is proportional to the expression differential. Unchanged, constitutive expression (1:1 ratio of experimental to control expression) shows as a neutral black.

             In the linked theoretical example, cDNA microarrays are  used to measure life-stage and tissue specific patterns of gene expression.