Exploring plant–microbe interactions using DNA microarrays
Box 1 The DNA array technique
The DNA array technique is in principle very simple. Thousands of DNA sequences (typically presynthesized oligonucleotides or inserts from cDNA libraries) are printed onto glass slides or nylon sheets using a robotic arrayer. To compare the abundance of these genes in a sample, RNA or DNA is extracted (the ‘target’), labelled and hybridized to the arrayed DNA (the ‘probe’). After washing, the probe is detected by fluorescence scanning or phosphor imaging. The primary data in microarray experiments consist of scans of the array (images). The spots on the images are quantified and the intensities are normalized. The final step is to identify genes that are significantly up- or down-regulated and to identify clusters of coregulated genes (regulons). The rationale behind the approach is that genes displaying similarity in expression pattern might be functionally related and governed by the same genetic control mechanism (Brown & Botstein, 1999).