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