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Array Analysis: The Basics

available from commercial manufacturers although many labs prepare their own arrays with the help of robotic arrayers. The methods of probe labeling, hybridization, and detection depend on the solid support to which the sequences are bound.

Many terms exist for naming gene arrays, including biochip, DNA chip, GeneChip (a registered trademark of Affymetrix, Inc.), DNA array, microarray and macroarray. Generally when biochip, DNA chip or GeneChip is used, it refers to arrays on glass supports. Microarray and macroarray may be used to differentiate between spot size or the number of spots on the support. Gene arrays may be used for sequence identification (e.g. mutation analysis) or differential expression analysis of two or more RNA samples. This discussion will focus on the use of arrays for expression analysis.


Gene Arrays for Expression Analysis
Gene arrays have become a powerful approach for comparing complex sample RNA populations. Using array analysis, the expression profiles of normal and tumor tissues, treated and untreated cell cultures, developmental stages of an organism or tissue, and different tissues can be compared. A typical gene array experiment involves:
  1. Isolating RNA from the samples to be compared
  2. Converting the RNA samples to labeled cDNA via reverse transcription; this step may be combined with aRNA amplification
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