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.
