A DNA microarray experiment compares gene expression between two populations. The DNA microarray chip contains a collection of thousands of microscopic DNA spots, termed probes, attached to a solid surface. Common microarrays contain probes corresponding to 20,000-40,000 genes. Other types of arrays include the exon arrays and the miRNA arrays which contain probes unique to all exons in the genome or to miRNAs respectively.
In the microarray technique, RNA is isolated from cells or tissues (A) and reverse transcribed to cDNA (B). At this stage, the cDNA is labeled and then hybridized to a microarray (C). The more copies a specific transcript has in the RNA sample, the stronger the staining intensity will be. The microarray is then scanned to quantify the staining intensity in each spot, which enables calculation of the relative gene expression. (D). In current illustration, the gene marked pink has a higher expression in sample A, the gene marked green in sample B and there is equal expression of the yellow-marked gene in both samples.