Abstract
Multiple expansion microscopy approaches have been successfully used in the analysis of centrioles, centrosomes, and cilia, helping to reveal the localization of numerous centrosomal and ciliary proteins at nanoscale resolution. In this chapter, we describe the use of two stable STED dyes in combination with expansion microscopy, which allows the robust detection by conventional and STED microscopy of proteins immunolabeled prior to sample expansion. We demonstrate the stability of these dyes during the crosslinking, polymerization, and denaturation steps of an expansion protocol thereby allowing their use in an immunolabel-first-expand-later approach. Our protocol overcomes the frequent technical limitation of poor, unreproducible binding of primary antibodies to proteins after denaturation. We demonstrate the applicability of this approach by analyzing both a centriole appendage protein Cep164 and a ciliary protein ARL13B.