book chapter published yes David Vijatovic author cf391e77-ec3c-11ea-a124-d69323410b580000-0002-5494-0941 Stavros Papadopoulos author 40606b92-f128-11eb-9611-bf66a98cfa5c Marco Dalla Vecchia author 02a7a869-ff06-11ed-a87f-86649d6077e5 Lora Beatrice Jaeger Sweeney author 56BE8254-C4F0-11E9-8E45-0B23E66974250000-0001-9242-5601 Caroline W.Beck editor LoSw department GradSch department IAS department Development and Evolution of Tetrapod Motor Circuits project Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity project Neuronal circuits in health and disease (Sweeney) project Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis project A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb transition of Xenopus metamorphosis project 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. https://research-explorer.ista.ac.at/download/22925/22938/2026_MIMB_Vijatovic.pdf application/pdfno Springer2026 eng mRNA FISHHybridization chain reactionIn situ hybridizationFluorescence microscopy 1940-6029 4268122810.1007/978-1-0716-5360-9_11 3049245-259 D. Vijatovic, S. Papadopoulos, M. Dalla Vecchia, L.B. Sweeney, in:, C.W. Beck (Ed.), Xenopus, Springer, 2026, pp. 245–259. Vijatovic D, Papadopoulos S, Dalla Vecchia M, Sweeney LB. 2026.Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In: Xenopus. Methods in Molecular Biology, vol. 3049, 245–259. D. Vijatovic, S. Papadopoulos, M. Dalla Vecchia, and L. B. Sweeney, “Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections,” in <i>Xenopus</i>, vol. 3049, C. W. Beck, Ed. Springer, 2026, pp. 245–259. Vijatovic, D., Papadopoulos, S., Dalla Vecchia, M., &#38; Sweeney, L. B. (2026). Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In C. W. Beck (Ed.), <i>Xenopus</i> (Vol. 3049, pp. 245–259). Springer. <a href="https://doi.org/10.1007/978-1-0716-5360-9_11">https://doi.org/10.1007/978-1-0716-5360-9_11</a> Vijatovic, David, et al. “Fluorescent in Situ MRNA Hybridization (FISH) Using Hybridization Chain Reaction (HCR) in Xenopus Cryosections.” <i>Xenopus</i>, edited by Caroline W. Beck, vol. 3049, Springer, 2026, pp. 245–59, doi:<a href="https://doi.org/10.1007/978-1-0716-5360-9_11">10.1007/978-1-0716-5360-9_11</a>. 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> Vijatovic, David, Stavros Papadopoulos, Marco Dalla Vecchia, and Lora B. Sweeney. “Fluorescent in Situ MRNA Hybridization (FISH) Using Hybridization Chain Reaction (HCR) in Xenopus Cryosections.” In <i>Xenopus</i>, edited by Caroline W. Beck, 3049:245–59. MIMB. Springer, 2026. <a href="https://doi.org/10.1007/978-1-0716-5360-9_11">https://doi.org/10.1007/978-1-0716-5360-9_11</a>. 229252026-09-13T22:01:55Z2026-09-17T07:31:16Z