Making and using spotted DNA microarrays in an academic core laboratory

Since its major launch into academia in the mid-1990s, spotted DNA microarray technology has expanded and matured into an important mainstream tool for genomic-scale gene expression studies across many species with many applications. Based on the principles of enzymatic nucleic acid labeling and DNA hybridization, the basic techniques were initially developed and disseminated by Patrick Brown's laboratory at Stanford and by others using "open source" approaches to techniques and instrumentation. Accessibility of microarrays has now become an important component of institutional research support. Indeed, the challenge facing many investigators when designing genome-scale experiments is to choose an appropriate platform and method from among the many microarray options available to them, both commercial and academic. The combination of microarray instrumentation and methods used for gene expression studies vary tremendously at different institutions and yet together function equally well as a whole. Instead of presenting a definitive set of instrumentation and methods, this chapter describes one such functional solution. It describes the specific implementation of instrumentation, standard operating procedures, and approaches for microarray fabrication and gene expression studies that are used routinely at the Microarray Resource within the W. M. Keck Biotechnology Resource Laboratory at Yale. The procedures have evolved through 6 years of operation and have resulted in at least 50 publications acknowledging the use of microarray slides and/or services provided by the Resource. The protocols that are presented for array fabrication, quality control, labeling, and hybridization utilize both "home-brew" and commercially available products to achieve an optimized set of cost-effective tools. The aim is to provide a compendium of approaches and protocols to aid those starting out on the core laboratory path and to provide insight into the types of microarray services and studies that are undertaken in this particular academic core laboratory.