In Situ Hybridization Protocols

ISBN-13: 9781071606223 / Angielski / Twarda / 2020 / 392 str.

Boye Nielsen; Julia Jones

Spis treści

Preface…
Table of Contents…
Contributing Authors…

Part I General Applications

1. Guidelines for the Optimization and Validation of In Situ Hybridization 
William J. Howat and Julia Jones

2. Overcoming Autofluorescence (AF) and Tissue Variation in Image Analysis of In Situ Hybridization
Cara Brodie 

Part II Methods for DNA ISH

3. Practical Application of Fluorescent In Situ Hybridization Techniques in Clinical Diagnostic Laboratories
Sheila J.M. O’Connor, Kathryn R. Turner, and Sharon L. Barrans

4. Fluorescent In Situ Hybridization using Oligonucleotide-Based Probes
Guilherme T. Braz, Fan Yu, Lívia do Vale Martins, and Jiming Jiang

5. Visualizing Genome Reorganization using 3D DNA FISH
Alasdair Jubb and Shelagh Boyle

Part III Methods for Cultured Cells

6. MicroRNA In Situ Hybridization in Paraffin Embedded Cultured Cells
Jaslin P. James, Laura Johnsen, Trine Møller, and Boye S. Nielsen

7. Multiplexed Detection and Analysis of Low Abundant Abundance Long Non-Coding RNA using RNAscopeTM in Cultured Cells
Julia Jones, Heather Zecchini, and Sankari Nagarajan

8. Multiplexed Quantitative In Situ Hybridization for Mammalian or Bacterial Cells in Suspension: qHCR Flow Cytometry (v3.0)
Maayan Schwarzkopf, Harry M.T. Choi, and Niles A. Pierce

9. Multiplexed Quantitative In Situ Hybridization for Mammalian Cells on a Slide: qHCR and dHCR Imaging (v3.0)
Maayan Schwarzkopf, Harry M.T. Choi, and Niles A. Pierce

Part IV Methods for Wholemounts and Plant Material

10. Multiplexed Quantitative In Situ Hybridization with Subcellular or Single-Molecule Resolution within Whole-Mount Vertebrate Embryos: qHCR and dHCR imaging (v3.0)
Harry M.T. Choi, Maayan Schwarzkopf, and Niles A. Pierce

11. Hybridization Chain Reaction for Quantitative and Multiplex Imaging of Gene Expression in Amphioxus Embryos and Adult Tissues
Toby G.R. Andrews, Giacomo Gattoni, Lara Busby, Michael A. Schwimmer, and Èlia Benito-Gutiérrez

12. RNAscopeTM Multiplex Detection in Zebrafish
Theresa Gross-Thebing 

13. Duplex In Situ Hybridization of Virus Nucleic Acids in Plant Tissues using RNAscopeTM
Samar Sheat, Stephan Winter, and Paolo Margaria

Part V Automated Methods for RNA

14. Automated ISH for Validated Histological Mapping of Lowly Expressed Genes
Charles Pyke 

15. Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping
Kenny Roberts and Omer Ali Bayraktar

16. Automated Co-In Situ Hybridization and Immunofluorescence using Archival Tumor Tissue Leah K. Officer, Kleopatra E. Andreou, Ana V. Teodósio, Zhangyi He,  and John P. Le Quesne

17. Automated 5-Color Multiplex Co-Detection of MicroRNA and Protein Expression in Fixed Tissue Specimens
Lorenzo F. Sempere, Erin Zaluzec, Elizabeth Kenyon, Matti Kiupel, and Anna Moore

18. Mixed Multiplex Staining: Automated RNAscopeTM and OPALTM for Multiple Targets
Michael Millar 

Part VI Multiplexing and Combined Methods

19. Simultaneous Visualization of RNA and Protein Expression in Tissue Using a Combined RNAscopeTM In Situ Hybridization and Immunofluorescence Protocol
Anushka Dikshit, Hailing Zong, Courtney Anderson, Bingqing Zhang, and Xiao-Jun Ma

20. In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections
Markus M. Hilscher, Daniel Gyllborg, Chika Yokot, and Mats Nilsson

21. GeoMx™ RNA Assay: High Multiplex, Digital, Spatial Analysis of RNA in FFPE Tissue
Daniel R. Zollinger, Stan E. Lingle, Kristina Sorg, Joseph M. Beechem, and Christopher R. Merritt

Part VII Target Selective Methods and Single Molecule Detection

22. In Situ Point Mutation Detection in FFPE Colorectal Cancers using the BaseScope Assay
Ann-Marie Baker and Trevor A. Graham 

23. Using In Situ Padlock Probe Technology to Detect mRNA Splice Variants in Tumor Cells
Lilli Hofmann, Thomas Kroneis, and Amin El-Heliebi 

24. Automated One-Double-Z Pair BaseScope™ for CircRNA In Situ Hybridization
Boye Schnack Nielsen, Trine Møller, and Jørgen Kjems

Blurb

This fifth edition volume expands on the previous editions with updated discussions on the many new in situ hybridization (ISH) techniques used by researchers today. New developments in probe designs, detection systems, specificity and sensitivity improvements, and multiplexing combinations are explored. Chapters in this book are organized into seven sections and cover general applications; methods for DNA ISH; methods for cultured cells; methods for wholemount and plant material; automated methods for RNA; multiplexing and combined methods; and targeted selective methods and single molecule detections. 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, In Situ Hybridization Protocols, Fifth Edition is a valuable resource for both novice and expert scientists interested in learning more about this exciting and advancing field.