A brief protocol for high-resolution whole mount in situ hybridization in zebrafish

Whole mount in situ hybridization (WISH) is a popular technique that is used to study temporal-spatial gene expression at mRNA level in model systems. Sensitive and high-resolution WISH is important for every laboratory that uses this technique to study expression pattern of genes in wildtype and perturbed embryos. Based on the commonly used protocols in fish community, our lab optimizes them to get more sensitive and specific results. Here, we briefly summarize the history of this technology using zebrafish as an example, describe a detailed experimental protocol, and provide troubleshooting for imperfect results and their solution.