[{"das_tickbox":"0","type":"book_chapter","series_title":"MIMB","citation":{"mla":"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>.","apa":"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>","short":"D. Vijatovic, S. Papadopoulos, M. Dalla Vecchia, L.B. Sweeney, in:, C.W. Beck (Ed.), Xenopus, Springer, 2026, pp. 245–259.","ieee":"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.","ama":"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>","chicago":"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>.","ista":"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."},"date_created":"2026-09-13T22:01:55Z","scopus_import":"1","day":"02","title":"Fluorescent in situ mRNA hybridization (FISH) using Hybridization Chain Reaction (HCR) in Xenopus cryosections","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["mRNA FISH","Hybridization chain reaction","In situ hybridization","Fluorescence microscopy"],"status":"public","department":[{"_id":"LoSw"},{"_id":"GradSch"},{"_id":"IAS"}],"date_published":"2026-09-02T00:00:00Z","file_date_updated":"2026-09-17T07:28:53Z","has_accepted_license":"1","acknowledgement":"This work was supported by a Horizon Europe ERC Starting Grant\r\nNumber 101041551 (L.B.S., D.V., S.P.), Special Research Program\r\n(SFB) of the Austrian Science Fund (FWF) F7814-B (L.B.S., S.P.),\r\nAustrian Science Fund (FWF) 10.55776/COE16 (L.B.S.), FTI\r\nStrategy Lower Austria Dissertation Grant Number FT121-D-046\r\n(D.V.), and Austrian Academy of Sciences DOC Fellowship 27229\r\n(S.P.). We also thank the Imaging & Optics and Scientific Computing Facilities at ISTA for their support in developing the quantification pipeline.","researchdata_availability":"no","_id":"22925","abstract":[{"lang":"eng","text":"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."}],"year":"2026","volume":3049,"file":[{"date_updated":"2026-09-17T07:28:53Z","success":1,"checksum":"e7a075a9ee1b91d5824f8f2b9b1f3c9b","file_id":"22938","file_size":1004024,"file_name":"2026_MIMB_Vijatovic.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-09-17T07:28:53Z"}],"page":"245-259","external_id":{"pmid":["42681228"]},"oa_version":"Published Version","OA_place":"publisher","quality_controlled":"1","date_updated":"2026-09-17T07:31:16Z","supplementarymaterial":"no","publication":"Xenopus","publisher":"Springer","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"editor":[{"last_name":"Beck","first_name":"Caroline W.","full_name":"Beck, Caroline W."}],"publication_identifier":{"eissn":["1940-6029"]},"alternative_title":["Methods in Molecular Biology"],"oa":1,"pmid":1,"article_processing_charge":"No","corr_author":"1","fulldoi":"https://doi.org/10.1007/978-1-0716-5360-9_11","doi":"10.1007/978-1-0716-5360-9_11","month":"09","intvolume":"      3049","publication_status":"published","ddc":["570"],"OA_type":"hybrid","language":[{"iso":"eng"}],"project":[{"grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","grant_number":"F7814","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e"},{"grant_number":"COE16","name":"Neuronal circuits in health and disease (Sweeney)","_id":"cf428362-b037-11f1-b015-8277a8a2f63d"},{"grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis","_id":"bd73af52-d553-11ed-ba76-912049f0ac7a"},{"name":"A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb transition of Xenopus metamorphosis","grant_number":"27229","_id":"907b765e-16d5-11f0-9cad-fef108a945b1"}],"author":[{"id":"cf391e77-ec3c-11ea-a124-d69323410b58","orcid":"0000-0002-5494-0941","first_name":"David","last_name":"Vijatovic","full_name":"Vijatovic, David"},{"full_name":"Papadopoulos, Stavros","first_name":"Stavros","last_name":"Papadopoulos","id":"40606b92-f128-11eb-9611-bf66a98cfa5c"},{"full_name":"Dalla Vecchia, Marco","first_name":"Marco","last_name":"Dalla Vecchia","id":"02a7a869-ff06-11ed-a87f-86649d6077e5"},{"full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","orcid":"0000-0001-9242-5601","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}]}]