Microarrays have helped researchers gain much insight into gene expression
profiles in the context of many diseases including those in the injured
heart. Our genomic investigations have been focused on elucidation of host
gene responses to enterovirus infection. We have gained valuable technical
expertise in using Affymetrix oligonucleotide arrays, also known as
GeneChips, and cDNA spotted arrays to probe differential gene expression in
both cultured cells and in heart tissue. Here, we provide a technique-focused
supplement to the Affymetrix GeneChip Expression Analysis Manual for sample
preparation, processing, and array hybridization. We provide expanded
explanations to highlight important points within the existing protocol and
offer variations to standard procedures when appropriate. For investigators
using myocardial tissues for microarray experiments, we further address the
necessity of and methods for in situ flushing of the vasculature, tissue
homogenization, and considerations for limits of expression detection in rare
cells. It is our intention to provide useful technical information, based on
our experience, to assist those researchers using Affymetrix GeneChips in
their own genomic research.