Automated liquid handling and high-throughput preparation of polymerase chain reaction-amplified DNA for microarray...

Genome-wide studies of gene expression and transcription factor-binding sites using DNA microarrays are leading to new systems level insights. The massively parallel nature of microarrays presents technical challenges: fabricating high-quality microarrays at the front end and data analysis and interpretation downstream. A principal challenge in fabricating microarrays is preparation of the DNA samples. This is particularly the case for polymerase chain reaction-amplified DNA samples. The challenge is to scale up efficiently to high-throughput preparation of tens of thousands of DNA samples while ensuring a uniform high quality. This chapter outlines strategic considerations, including automated liquid handling and workflow development to maximize efficiency, and quality control (QC) measures to ensure uniform quality. The protocols are presented with commentary to illustrate their logic and specific techniques. These principles and techniques are extensible to other high-throughput molecular biological applications.