Profiling Gene Expression Signatures Using Fluorescent Microspheres

One of the primary goals of genome-wide expression profiling is to identify subsets of gene transcripts that can be associated with specific biological conditions. Once these gene expression “signatures” have been elucidated, they can be used in screening assays to identify compounds that induce similar gene expression changes. To increase the throughput of these screening assays, we have optimized the development of a fluorescent microsphere–based, flow cytometric platform that allows the specific and sensitive screening of up to 100 transcripts per sample in a 96-well plate format. This chapter will outline experimental details of such an experiment using an estrogenic gene expression signature as a specific example.