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Updated: Dec 21, 2025
Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization
Published on: March 25, 2009
Multiplexed Quantitative In Situ Hybridization with Subcellular or Single-Molecule Resolution Within Whole-Mount
Harry M T Choi1, Maayan Schwarzkopf1, Niles A Pierce2,3,4
1Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Abstract:
In situ hybridization based on the mechanism of hybridization chain reaction (HCR) enables multiplexed quantitative mRNA imaging in the anatomical context of whole-mount vertebrate embryos. Third-generation in situ HCR (v3.0) provides automatic background suppression throughout the protocol, dramatically enhancing performance and ease of use. In situ HCR v3.0 supports two quantitative imaging modes: (1) qHCR imaging for analog mRNA relative quantitation with subcellular resolution in an anatomical context and (2) dHCR imaging for digital mRNA absolute quantitation with single-molecule resolution in an anatomical context. Here, we provide protocols for qHCR and dHCR imaging in whole-mount zebrafish, chicken, and mouse embryos.
