Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections

Vijatovic, David; Papadopoulos, Stavros; Dalla Vecchia, Marco; Sweeney, Lora Beatrice Jaeger

Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections

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.

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2026_MIMB_Vijatovic.pdf 1.00 MB [Published Version]

DOI

10.1007/978-1-0716-5360-9_11

Book Chapter | Published | English

Scopus indexed

Author

Vijatovic, David^ISTA ; Papadopoulos, Stavros^ISTA; Dalla Vecchia, Marco^ISTA; Sweeney, Lora B.^ISTA

Book Editor

Beck, Caroline W.

Corresponding author has ISTA affiliation

Department

Sweeney Group
Graduate School
Image Analysis Services

Grant

Development and Evolution of Tetrapod Motor Circuits
Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity
Neuronal circuits in health and disease (Sweeney)
Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis
A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb transition of Xenopus metamorphosis

Series Title

Methods in Molecular Biology

Abstract

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.

Keywords

mRNA FISH; Hybridization chain reaction; In situ hybridization; Fluorescence microscopy

Publishing Year

2026

Date Published

2026-09-02

Book Title

Xenopus

Publisher

Springer

Acknowledgement

This work was supported by a Horizon Europe ERC Starting Grant Number 101041551 (L.B.S., D.V., S.P.), Special Research Program (SFB) of the Austrian Science Fund (FWF) F7814-B (L.B.S., S.P.), Austrian Science Fund (FWF) 10.55776/COE16 (L.B.S.), FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.), and Austrian Academy of Sciences DOC Fellowship 27229 (S.P.). We also thank the Imaging & Optics and Scientific Computing Facilities at ISTA for their support in developing the quantification pipeline.

Volume

3049

Page

245-259

eISSN

1940-6029

IST-REx-ID

22925

Cite this

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. Xenopus. Vol 3049. MIMB. Springer; 2026:245-259. doi:10.1007/978-1-0716-5360-9_11

Vijatovic, D., Papadopoulos, S., Dalla Vecchia, M., & Sweeney, L. B. (2026). Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections. In C. W. Beck (Ed.), Xenopus (Vol. 3049, pp. 245–259). Springer. https://doi.org/10.1007/978-1-0716-5360-9_11

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 Xenopus, edited by Caroline W. Beck, 3049:245–59. MIMB. Springer, 2026. https://doi.org/10.1007/978-1-0716-5360-9_11.

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 Xenopus, vol. 3049, C. W. Beck, Ed. Springer, 2026, pp. 245–259.

Vijatovic, David, et al. “Fluorescent in Situ MRNA Hybridization (FISH) Using Hybridization Chain Reaction (HCR) in Xenopus Cryosections.” Xenopus, edited by Caroline W. Beck, vol. 3049, Springer, 2026, pp. 245–59, doi:10.1007/978-1-0716-5360-9_11.

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