A method of in situ hybridization combined with immunocytochemistry, histochemistry, and tract tracing to characterize the mRNA expressing cell types in heterogeneous neuronal populations.

A rapid, sensitive, non-isotopic in situ hybridization histochemistry protocol is presented to study the expression of mRNA at the single cell level in anatomically complex structures of the mammalian central nervous system. The protocol uses digoxigenin-UTP-labeled riboprobes, freefloating sections, and alkaline phosphatase and horseradish peroxidase detection. Modifications have been introduced which preserve the integrity of marker molecules, and as such enable the simultaneous identification and characterization of CNS cell types by tract tracing, histochemical, and immunocytochemical detection of intra- and extracellular markers. All pretreatments that enhance probe penetration have been omitted without substantial loss in sensitivity. The protocol has been successfully extended to vibratome sections with subsequent plastic-embedding and semithin sectioning, which considerably broadens the general applicability of this fast and easy ISHH method.