Isolation of O3-response genes from Arabidopsis thaliana using cDNA macroarray

Nylon membrane-based cDNA macroarrays are a widely available alternative to cDNA microarrays for the collection of large-scale gene expression data. cDNA macroarrays are used in many areas of molecular biology research for applications ranging from gene discovery to gene expression profiling. Although degree of location of DNA spot in cDNA macroarray is lower than that in cDNA microarray, it can be used to detect expression of a large number of genes because it uses radiolabeled cDNA as a probe. Thus, cDNA macroarray technology can be applied to obtain the gene expression profile in organs that show wide variety in mRNA expression, such as meristems in plant species and brain tissue. To carry out hybridization experiments with a cDNA macroarray, I describe here how to prepare macroarray filters on a small or large scale, as well as how to analyze macroarray experiments and determine the statistical significance of the gene expression data obtained.