Microarray mRNA expression profiling to study cystic fibrosis

Shyam Ramachandran; Luka A Clarke; Todd E Scheetz; Margarida D Amaral; Paul B McCray Jr

doi:10.1007/978-1-61779-120-8_12

Back

Journal article

Microarray mRNA expression profiling to study cystic fibrosis

Shyam Ramachandran, Luka A Clarke, Todd E Scheetz, Margarida D Amaral and Paul B McCray Jr

Methods in molecular biology (Clifton, N.J.), Vol.742, pp.193-212

2011

DOI: 10.1007/978-1-61779-120-8_12

PMID: 21547734

View Online

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.

Gene Expression

Genes

Phenotype

Mutation

Genetic Association Studies

RNA, Messenger - isolation & purification

Oligonucleotide Array Sequence Analysis - methods

Cystic Fibrosis - physiopathology

Humans

Databases, Genetic

Gene Expression Profiling - methods

Cystic Fibrosis Transmembrane Conductance Regulator - metabolism

Genetic Phenomena

RNA, Messenger - biosynthesis

Analysis of Variance

Cystic Fibrosis - genetics

Cystic Fibrosis Transmembrane Conductance Regulator - genetics

Details

Title: Subtitle: Microarray mRNA expression profiling to study cystic fibrosis
Creators: Shyam Ramachandran - Interdisciplinary Program in Genetics, Department of Pediatrics, University of Iowa, Iowa City, IA, USA. shyam-ramachandran@uiowa.edu
Luka A Clarke
Todd E Scheetz
Margarida D Amaral
Paul B McCray Jr
Resource Type: Journal article
Publication Details: Methods in molecular biology (Clifton, N.J.), Vol.742, pp.193-212
DOI: 10.1007/978-1-61779-120-8_12
PMID: 21547734
NLM abbreviation: Methods Mol Biol
eISSN: 1940-6029
Publisher: United States
Language: English
Date published: 2011
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Microbiology and Immunology; Pulmonary Medicine; Stead Family Department of Pediatrics; Internal Medicine; Ophthalmology and Visual Sciences
Record Identifier: 9983980060802771

Metrics

23 Record Views

11 Times Cited - Web of Science