Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections Methods in Molecular Biology Vijatovic, David ; https://orcid.org/0000-0002-5494-0941 Papadopoulos, Stavros Dalla Vecchia, Marco Sweeney, Lora Beatrice Jaeger ; https://orcid.org/0000-0001-9242-5601 Beck, Caroline W. mRNA FISH Hybridization chain reaction In situ hybridization Fluorescence microscopy ddc:570 Hybridization Chain Reaction (HCR) enables highly sensitive and multiplexed detection of mRNA with subcellular spatial resolution. It employs fluorophore-tagged DNA hairpins that self-assemble on target-bound probe pairs, amplifying the signal without enzymatic reactions. Here, we describe a protocol for performing HCR fluorescence in situ hybridization (FISH) on Xenopus tissue sections. We also outline a semi-automated image analysis pipeline that enables per-cell quantification of probe expression and co-localization. This method provides a robust and quantitative approach for visualizing gene expression patterns in situ. Springer 2026 info:eu-repo/semantics/bookPart doc-type:BookPart BookPart http://purl.org/coar/resource_type/c_3248 https://research-explorer.ista.ac.at/record/22925 https://research-explorer.ista.ac.at/download/22925/22938 Vijatovic D, Papadopoulos S, Dalla Vecchia M, Sweeney LB. Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In: Beck CW, ed. <i>Xenopus</i>. Vol 3049. MIMB. Springer; 2026:245-259. doi:<a href="https://doi.org/10.1007/978-1-0716-5360-9_11">10.1007/978-1-0716-5360-9_11</a> eng info:eu-repo/semantics/altIdentifier/doi/10.1007/978-1-0716-5360-9_11 info:eu-repo/semantics/altIdentifier/e-issn/1940-6029 info:eu-repo/semantics/altIdentifier/pmid/42681228 https://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess