Microarray mRNA expression profiling to study cystic fibrosis.

Abstract To understand the links between CFTR mutations and the development of cystic fibrosis (CF) pheno-types, it is imperative to study the transcriptome in affected cell types. Microarray expression profilingprovides a platform to study global gene expression in detail. This approach may provide the necessaryinformation to segregate phenotypic characteristics of CF, differentiate between genetic or environmen-tal factors, and assess the advent and progression of disease phenotypes. Moreover, if a “CF signature”of genes with altered expression is defined, this can be used to monitor effectiveness of treatment. Weprovide here detailed protocols and tips for collecting and preserving tissues and cells, and preparingtotal RNA. We also outline novel strategies for experimental design and data analysis, and describe somepowerful gene and pathway discovery tools. Key words: GeneChip, mRNA, hybridization, Gene set enrichment analysis, Ingenuity pathwayanalysis, ANOVA, GeneGo, normalization, quality control, differential expression.