The following chapter describes a miniaturized array-based platform for RNAi screening. The PhenomicID™ platform combines high density spotted microarray technology, high content imaging of the cells, and computational algorithms for image and data analysis. This platform provides an efficient and cost effective way to use reverse genetic tools for analysis of mammalian gene functions on a genome-wide scale. The miniaturization of this process allows for experimental complexity and applications not previously feasible when performed in a well-based format. Our team has employed this technology to identify functional genes involved in the progression of infectious diseases, in cell-based infectious models for HIV, Chagas, Dengue virus, Chikungunya virus, and Influenza virus. Importantly, the power of miniaturized technologies is not limited to screening of RNAi libraries, but can allow performance of complex experiments - combining drug and siRNA treatments to identify drug targets. In addition the flexibility of the describe platform allows researchers to profile multiple primary cell lines in search for essential genes. In this chapter we will discuss practical guidance for developing microarray-based genome-wide library siRNA screening and its applications.
Keywords: Assay optimization, data analysis, image analysis, infectious disease, microarray printing, reverse transfection, siRNA screening, ultra-high throughput.