Performing SABER-FISH on Chromosome Spreads in Fixed Tissue Culture Cells and in Tissues

Fluorescence in situ hybridization (FISH) visualizes targeted nucleic acid sequences in fixed samples, imparting information about target location and abundance. By itself, targets are limited to large regions or those with high copy number due to low fluorescent signal, motivating a need for signal amplification methods. In this chapter, we detail signal amplification by exchange reaction (SABER), a recent advancement in FISH technology that incorporates long, repetitive concatemers into FISH probes to recruit complementary fluorescent probes. The additional binding sites on the concatemers result in a 5- to 450-fold boost in RNA and DNA FISH signals, unlocking the potential to target smaller regions. This method offers a rapid, versatile, and cost-effective approach for multiplexed nucleic acid imaging. By incorporating SABER into FISH protocols, researchers can achieve high sampling efficiency and overcome the limitations of traditional FISH techniques. This chapter aims to describe the SABER FISH technology and provide detailed steps for applying RNA and DNA SABER FISH to a variety of samples, including on metaphase spreads, cells, and tissues (FFPE and fixed cryosections) across mouse and human specimens.