Profiling Gene Expression in African Turquoise Killifish Nothobranchius furzeri Embryos with RNA Fluorescence In Situ Hybridization Chain Reaction (HCR)

Gene expression profiles reveal the dynamic behavior of gene products and provide key information to correlate genetic regulation and phenotypical functions. To obtain gene expression profiles with high performance, RNA fluorescence in situ hybridization chain reaction (HCR) was developed from traditional fluorescence in situ hybridization (FISH), with the abilities of orthogonal signal amplification and automatic background suppression. Experimentally, these features yield unique advantages including dramatically improved signal-to-noise ratio, simultaneous multiplexing, high specificity, and single-molecule sensitivity. Here, we demonstrate HCR in the whole-mount embryos of African turquoise killifish Nothobranchius furzeri. The goal is to elaborate this ease-of-use technique and present a robust protocol applicable to emerging research organisms beyond African turquoise killifish.