Protocol

Cystic Fibrosis

Volume 742 of the series Methods in Molecular Biology pp 193-212

Date:

Microarray mRNA Expression Profiling to Study Cystic Fibrosis

  • Shyam RamachandranAffiliated withInterdisciplinary Program in Genetics, Department of Pediatrics, University of Iowa
  • , Luka A. ClarkeAffiliated withFaculty of Sciences, BioFIG-Centre for Biodiversity, Functional and integrative Genomics, University of Lisboa
  • , Todd E. ScheetzAffiliated withDepartment of Ophthalmology and Visual Sciences, Interdisciplinary Program in Genetics, University of Iowa
  • , Margarida D. AmaralAffiliated withFaculty of Sciences, BioFIG-Centre for Biodiversity, Functional and integrative Genomics, University of LisboaDepartment of Genetics, Centre of Human Genetics, National Institute of Health
  • , Paul B. McCrayJrAffiliated withInterdisciplinary Program in Genetics, Department of Pediatrics, University of Iowa Email author 

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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.

Key words

GeneChip mRNA hybridization Gene set enrichment analysis Ingenuity pathway analysis ANOVA GeneGo normalization quality control differential expression