Tissue-specific gene expression is a major determinant in the elaboration of cells with distinctive phenotypes and functions, which is crucial for the development and homeostasis of multicellular organisms. Fluorescent in situ hybridization (FISH) is a powerful method for assessing the expression and localization properties of RNA at subcellular resolution in whole mount organism and tissue specimens. This chapter describes a high-resolution FISH protocol for the detection of RNA expression and localization dynamics in embryos and tissues of the fruit fly,Drosophila melanogaster. The approach utilizes tyramide signal amplification (TSA) for enhanced sensitivity and resolution in the detection of coding and noncoding RNAs, for the codetection of different RNA species or of RNA and a protein marker of interest. Furthermore, the protocol outlines details for conducting FISH in microtiter plates, which greatly enhances the throughput, practicality, and economy of the procedure.
