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Fluorescence In Situ Hybridization (FISH)

Methods and Protocols

  • Book
  • © 2024

Overview

Editors:
  1. Gal Haimovich

    1. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2784)

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About this book

This volume explores the latest techniques and protocols used by researchers to address unique biological questions, model organisms not typically studied by Fluorescent In Situ Hybridization (FISH), protocols combining FISH with immunofluorescence (FISH-IF), and high-throughput experiments. The chapters in this book are divided into two parts: RNA FISH protocols and DNA FISH protocols. Part One covers methods for designing OligoPaint probes and studying distinct aspects of RNA biology such as transcription and splicing dynamics, and mRNA and small RNA expression and localization. Part Two discusses DNA repair dynamics, gene compaction, and chromatin conformation and gene rearrangements in plants, insects, and mammalian cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting edge and thorough, Fluorescence In Situ Hybridization (FISH): Methods and Protocols is a valuable resource that will benefit the broader scientific community in their studies and understanding of this important field. 


Keywords

Table of contents (19 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. RNA FISH

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria

      • Camilla Ciolli Mattioli, Roi Avraham
      Pages 3-23

    3. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in the Fungal Pathogen Candida albicans

      • Sander van Otterdijk, Maryam Motealleh, Zixu Wang, Thomas D. Visser, Philipp Savakis, Evelina Tutucci
      Pages 25-44

    4. RNA and Protein Detection by Single-Molecule Fluorescent in Situ Hybridization (smFISH) Combined with Immunofluorescence in the Budding Yeast S. cerevisiae

      • Anna Maekiniemi, Robert H. Singer
      Pages 45-58

    5. Fluorescence In Situ Hybridization as a Tool for Studying the Specification and Differentiation of Cell Types in Nematostella vectensis

      • Océane Tournière, Henriette Busengdal, James M. Gahan, Fabian Rentzsch
      Pages 59-75

    6. SABER-FISH in Hydractinia

      • Miguel Salinas-Saavedra
      Pages 77-85

    7. smFISH for Plants

      • Sahar Hani, Caroline Mercier, Pascale David, Thierry Desnos, Jean-Marc Escudier, Edouard Bertrand et al.
      Pages 87-100

    8. Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH

      • Kun Huang, Blake C. Meyers, Jeffrey L. Caplan
      Pages 101-111

    9. hcHCR: High-Throughput Single-Cell Imaging of RNA in Human Primary Immune Cells

      • Manasi Gadkari, Jing Sun, Adrian Carcamo, Iain Fraser, Luis M. Franco, Gianluca Pegoraro
      Pages 113-132

    10. High-Throughput RNA-HCR-FISH Detection of Endogenous Pre-mRNA Splice Variants

      • Asaf Shilo, Gianluca Pegoraro, Tom Misteli
      Pages 133-146

    11. Simultaneous In Situ Detection of m6A-Modified and Unmodified RNAs Using DART-FISH

      • Charles J. Sheehan, Kate D. Meyer
      Pages 147-161

    12. Multiplexed Immunofluorescence and Single-Molecule RNA Fluorescence In Situ Hybridization in Mouse Skeletal Myofibers

      • Lance T. Denes, Chase P. Kelley, Eric T. Wang
      Pages 163-176

    13. Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP

      • Monika W. Perez, Conor K. Camplisson, Brian J. Beliveau
      Pages 177-189

    14. Efficient Prediction Model of mRNA End-to-End Distance and Conformation: Three-Dimensional RNA Illustration Program (TRIP)

      • Jiayun Ma, Tatsuhisa Tsuboi
      Pages 191-200

  3. DNA FISH

    1. Front Matter

      Pages 201-201
      Download chapter PDF

    2. Combined 3D DNA FISH, Single-Molecule RNA FISH, and Immunofluorescence

      • Souvik Sen, Shivnarayan Dhuppar, Aprotim Mazumder
      Pages 203-214

    3. Determining the Compaction State of Genes Using DNA FISH

      • Masako Narita, Ioana Olan, Masashi Narita
      Pages 215-225

    4. Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software

      • Jean-Bernard Fiche, Marie Schaeffer, Christophe Houbron, Christel Elkhoury Youhanna, Olivier Messina, Franziska Barho et al.
      Pages 227-257

    5. Rapid DNA-FISH in Arabidopsis thaliana Somatic Cells

      • Olga Raskina, Ofir Hakim
      Pages 259-270
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Editors and Affiliations

  • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel

    Gal Haimovich

Bibliographic Information

  • Book Title: Fluorescence In Situ Hybridization (FISH)

  • Book Subtitle: Methods and Protocols

  • Editors: Gal Haimovich

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3766-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3765-4Published: 20 March 2024

  • Softcover ISBN: 978-1-0716-3768-5Due: 20 April 2024

  • eBook ISBN: 978-1-0716-3766-1Published: 19 March 2024

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 302

  • Number of Illustrations: 1 b/w illustrations, 67 illustrations in colour

  • Topics: Biochemistry, general, Genetics and Genomics

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