Two-color detection of mRNA transcript localizations in fish and fly embryos using alkaline phosphatase and β-galactosidase conjugated antibodies

A fast and simplified two-color in situ hybridization procedure for the simultaneous detection of two different mRNAs in whole-mounted zebrafish and Drosophila embryos is presented. Transcript distributions are detected in a single incubation step using a mixture of alkaline phosphatase and beta-galactosidase coupled antibodies. The different transcripts are visualized in contrasting colors by the use of beta-galactosidase substrates that develop color precipitates (magenta, blue) easily distinguishable from those of the standard alkaline phosphatase substrates. This protocol can be followed by standard immunohistochemistry to detect the expression of a third gene (at the protein level) in a third color.