Whole mount in situ hybridization (ISH) is a very informative approach for visualizing gene expression patterns over the entire embryo or tissue 3D structure. However, conventional whole mount ISH procedures are lengthy and require extensive optimization. During the last few years, our customers have shown very innovative approaches to applying the RNAscope™ ISH technology on whole mount samples:

Whole-mount in situ hybridization in zebrafish embryos
Gross-Thebing et al. were the first to publish the application of RNAscope™ ISH in whole mount zebrafish.

Combined RNAscope ISH-IHC in whole mouse inner ear
Kersigo et al. described a method for combining RNAscope™ ISH with IHC to study gene expression in a complex tissue, the whole mouse inner ear.

Dendrite shape and stability of wingless (WG) in drosophila embryos
Li et al. applied RNAscope™ ISH for the study of whole mount drosophila embryos

Verification of overexpression in whole Drosophila hearts
Another study in drosophila was done by Cannon et al. who applied RNAscope™ ISH on whole drosophila hearts.

Combined RNAscope ISH-IHC in whole mouse retinas
Dual RNAscope™ ISH-IHC in whole postnatal mouse retinas was performed by Ogura et al. to examine the effects of pericyte depletion on retinal blood vessel integrity.

3D in vivo molecular interrogation in cleared chick embryos
Morrison et al. combined RNAscope™ ISH, IHC, and FRUIT tissue clearing method to visualize and quantify transcripts and protein localization within single cells deep within intact chick embryos.