Construction of microarrays and their application to virus analysis

Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell

Full Citation: Allen, M. J., B. Tiwari, M. E. Futschik, and D. Lindell. 2010. Construction of microarrays and their application to virus analysis, p. 34-56. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. [DOI 10.4319/mave.2010.978-0-9845591-0-7.34]

ABSTRACT: DNA microarray is the term used to describe a microscopic collection of DNA probes arrayed onto a solid surface. Microarrays take advantage of the highly selective nature of nucleic acid interactions and are commonly used for expression profiling, for comparative genomic hybridization, to aid genomic annotation, and for detection of mutations within genomes. In this virus-focused chapter, we deal primarily with the use of microarrays for expression analysis (the most popular usage) of host and virus systems during infection. We examine aspects related to array platform choice (spotted and oligonucleotide arrays), probe and array design considerations, experimental procedures and data analysis, normalization, processing, and curation. We also provide in-depth examples for the study of viral transcriptome analysis for both spotted long oligonucleotide (coccolithoviruses) and Affymetrix GeneChip (cyanophage) arrays.