In Situ Hybridization Protocols [electronic resource]

  • Nielsen, Boye Schnack. editor. , Jones, Julia. editor.
  • Springer US : Imprint: Humana
  • 2020
In Situ Hybridization Protocols [electronic resource]


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.


General Applications
Guidelines for the Optimization and Validation of In Situ Hybridization / Julia Jones, William J. Howat
Overcoming Autofluorescence (AF) and Tissue Variation in Image Analysis of In Situ Hybridization / Cara Brodie

Methods for DNA ISH
Practical Application of Fluorescent In Situ Hybridization Techniques in Clinical Diagnostic Laboratories / Sheila J. M. O’Connor, Kathryn R. Turner, Sharon L. Barrans
Fluorescent In Situ Hybridization Using Oligonucleotide-Based Probes / Guilherme T. Braz, Fan Yu, Lívia do Vale Martins, Jiming Jiang
Visualizing Genome Reorganization Using 3D DNA FISH / Alasdair Jubb, Shelagh Boyle

Methods for Cultured Cells
MicroRNA In Situ Hybridization in Paraffin-Embedded Cultured Cells / Jaslin P. James, Laura Johnsen, Trine Møller, Boye Schnack Nielsen
Multiplexed Detection and Analysis of Low-Abundance Long Noncoding RNA Using RNAscope™ in Cultured Cells / Julia Jones, Heather Zecchini, Sankari Nagarajan
Multiplexed Quantitative In Situ Hybridization for Mammalian or Bacterial Cells in Suspension: qHCR Flow Cytometry (v3.0) / Maayan Schwarzkopf, Harry M. T. Choi, Niles A. Pierce
Multiplexed Quantitative In Situ Hybridization for Mammalian Cells on a Slide: qHCR and dHCR Imaging (v3.0) / Maayan Schwarzkopf, Harry M. T. Choi, Niles A. Pierce

Methods for Wholemounts and Plant Material
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, Niles A. Pierce
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, Èlia Benito-Gutiérrez
RNAscope™ Multiplex Detection in Zebrafish / Theresa Gross-Thebing
Duplex In Situ Hybridization of Virus Nucleic Acids in Plant Tissues Using RNAscope® / Samar Sheat, Stephan Winter, Paolo Margaria

Automated Methods for RNA
Automated ISH for Validated Histological Mapping of Lowly Expressed Genes / Charles Pyke
Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping / Kenny Roberts, Omer Ali Bayraktar
Automated Co-in Situ Hybridization and Immunofluorescence Using Archival Tumor Tissue / Leah K. Officer, Kleopatra E. Andreou, Ana V. Teodósio, Zhangyi He, John P. Le Quesne
Automated Five-Color Multiplex Co-detection of MicroRNA and Protein Expression in Fixed Tissue Specimens / Lorenzo F. Sempere, Erin Zaluzec, Elizabeth Kenyon, Matti Kiupel, Anna Moore
Mixed Multiplex Staining: Automated RNAscope™ and OPAL™ for Multiple Targets / Michael Millar

Multiplexing and Combined Methods
Simultaneous Visualization of RNA and Protein Expression in Tissue Using a Combined RNAscope™ In Situ Hybridization and Immunofluorescence Protocol / Anushka Dikshit, Hailing Zong, Courtney Anderson, Bingqing Zhang, Xiao-Jun Ma
In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections / Markus M. Hilscher, Daniel Gyllborg, Chika Yokota, Mats Nilsson
GeoMx™ RNA Assay: High Multiplex, Digital, Spatial Analysis of RNA in FFPE Tissue / Daniel R. Zollinger, Stan E. Lingle, Kristina Sorg, Joseph M. Beechem, Christopher R. Merritt

Target Selective Methods and Single Molecule Detection
In Situ Point Mutation Detection in FFPE Colorectal Cancers Using the BaseScope Assay / Ann-Marie Baker, Trevor A. Graham
Using In Situ Padlock Probe Technology to Detect mRNA Splice Variants in Tumor Cells / Lilli Hofmann, Thomas Kroneis, Amin El-Heliebi
Automated One-Double-Z Pair BaseScope™ for CircRNA In Situ Hybridization / Boye Schnack Nielsen, Trine Møller, Jørgen Kjems