Protocol for the use of signal amplification by exchange reaction-fluorescence in situhybridization on adult formalin-fixed paraffin-embedded mouse lung tissue

Fluorescence in situhybridization (FISH) is a useful tool for analyzing RNA expression, but difficulties arise with low-abundance RNA and in tissues that are formalin fixed paraffin embedded (FFPE) because reagents can be expensive. In this protocol, we adapt a previously designed FISH amplification protocol (SABER [signal amplification by exchange reaction])1for adult mouse FFPE lung sections by using probes that are extended and branched to amplify the signal. We combine FISH and immunostaining to identify cell-specific RNA.