Determining the expression pattern of a gene of interest is critical to understanding when, where, and how it may function during development. This chapter describes methods for determining the localization and expression levels for both mRNA and protein. Some of these methods can be described as quantitative or semi-quantitative while others are considered more qualitative in nature. To determine the spatial localization of mRNA expression, RNAin situhybridization can be used on both whole-mount or sectioned embryos. Northern blot and qPCR are more quantitative methods for analyzing mRNA expression levels. For determining protein localization, antibody staining either by immunocytochem-istry or immunofluorescence can be performed on both whole-mount or sectioned embryos; whereas Western blot is the method generally used for quantifying protein expression levels.
