title: Microarray mRNA expression profiling to study cystic fibrosis.
abstract: To understand the links between CFTR mutations and the development of cystic fibrosis (CF) phenotypes, it is imperative to study the transcriptome in affected cell types. Microarray expression profiling provides a platform to study global gene expression in detail. This approach may provide the necessary information to segregate phenotypic characteristics of CF, differentiate between genetic or environmental 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. We provide here detailed protocols and tips for collecting and preserving tissues and cells, and preparing total RNA. We also outline novel strategies for experimental design and data analysis, and describe some powerful gene and pathway discovery tools.
authors.affiliation: Interdisciplinary Program in Genetics, Department of Pediatrics, University of Iowa, Iowa City, IA, USA. shyam-ramachandran@uiowa.edu
authors.forename: Shyam
authors.initials: S
authors.lastname: Ramachandran
authors.forename: Luka A
authors.initials: LA
authors.lastname: Clarke
authors.forename: Todd E
authors.initials: TE
authors.lastname: Scheetz
authors.forename: Margarida D
authors.initials: MD
authors.lastname: Amaral
authors.forename: Paul B
authors.initials: PB
authors.lastname: McCray
mesh_terms: D000704:Analysis of Variance; D003550:Cystic Fibrosis / Q000235:genetics* / Q000503:physiopathology; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes; D056726:Genetic Association Studies; D055614:Genetic Phenomena; D006801:Humans; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D012333:RNA, Messenger / Q000096:biosynthesis / Q000302:isolation & purification*
chemical_list: D012333:RNA, Messenger; D019005:Cystic Fibrosis Transmembrane Conductance Regulator