Wholemount in situ Hybridization for Spatial-temporal Visualization of Gene Expression in Early Post-implantation Mouse Embryos

Regionalized distribution of genes plays crucial roles in the formation of the spatial pattern in tissues and embryos during development. In situ hybridization has been one of the most widely used methods to screen, identify, and validate the spatial distribution of genes in tissues and embryos, due to its relative simplicity and low cost. However, acquisition of high-quality hybridization signals remains a challenge while maintaining good tissue morphology, especially for small tissues such as early post-implantation mouse embryos. In this protocol, we present a detailed RNA in situ hybridization protocol suitable for wholemount early post-implantation mouse embryos and other small tissue samples. This protocol uses digoxigenin (DIG) labeled riboprobes to hybridize with target transcripts, alkaline phosphatase-conjugated anti-DIG antibodies to recognize DIG-labeled nucleotides, and nitroblue tetrazolium (NBT)/5-bromo-4-chloro-3-indolyl-phosphate (BCIP) chromogenic substrates for color development. Specific steps and notes on riboprobe preparation, embryo collection, probe hybridization, and color development are all included in the following protocol. Graphic abstract: Overview of Wholemount in situ Hybridization in Early Mouse Embryos.