This volume contains a comprehensive compilation of chromogenic and fluorescent RNA in situ hybridization (ISH) technology in many of its various shades, forms, and applications. The book is organized into a number of parts and chapters focusing on the application of ISH methodologies to different animal species as used in Evolutionary Development (EvoDevo) and Biomedical research, and covering new developments in RNA visualization by fluorescent ISH (FISH). The described (F)ISH protocols employ effective strategies for signal enhancement and target amplification allowing for high signal intensities and drastically improved signal-to-noise ratios. Chromogenic and fluorescent ISH, as specified in the various chapters, are most essential for RNA expression profiling, applied to many fields of research including cellular, developmental, and evolutionary biology, neurobiology and neuropathology. Written for the popular Neuromethods series, chapters include the kind of detail and key implementation advice that ensures successful results in the laboratory.Essential and authoritative, In Situ Hybridization Methods provides detailed protocols for newcomers to ISH, and inspires researchers familiar with the technique to seek and find up-to-date methodology for new and specialized applications.

Includes cutting-edge methods and protocols

Optimization of In Situ Hybridization and Co--Expression Analysis in the Central Nervous System.- In Situ Hybridization Methods for RNA Visualization in C. elegans.- Multicolored Visualization of Transcript Distributions in Drosophila Embryos.- Exploring Brain Genoarchitecture by Single and Double Chromogenic In Situ Hybridization (ISH) and Immunohistochemistry (IHC) in Whole-Mount Embryos.- Exploring Brain Genoarchitecture by Single and Double Chromogenic In Situ Hybridization (ISH) and Immunohistochemistry (IHC) on Cryostat, Paraffin, or Floating Sections.- Combined Radioactive and Non-Radioactive Double In Situ Hybridization (DISH).- One FISH, dFISH, three FISH:  Sensitive Methods of Whole-Mount Fluorescent In Situ Hybridization in Freshwater Planarians.- Whole-Mount In Situ Hybridization and Immunohistochemistry in Xenopus Embryos.- Manual and Automated Whole-Mount In Situ Hybridization for Systematic Gene Expression Analysis in Embryonic Zebrafish Forebrain.- Large-Scale ISH on Mouse Brain Sections for Systematic Gene Expression Analysis in Developing Mouse Diencephalon.- High-Throughput In Situ Hybridization: Systematical Production of Gene Expression Data and Beyond.- Analysis of Embryonic Gene Expression Patterns in the Hagfish.- Gene Expression Analysis of Lamprey Embryos.- Detection of mRNA and MicroRNA Expression in Basal Chordates, Amphioxus and Ascidians.- Analysis of Gene Expression in Neurons and Synapses by Multi-Color In Situ Hybridization.- Fluorescent In Situ Hybridization in Primary Hippocampal Neurons to Detect Localized mRNAs.- Combining Whole-Mount In Situ Hybridization with Neuronal Tracing and Immunohistochemistry.- Fluorescent In-Situ Hybridization Detection of MicroRNAs in Newt Tissue Cryosections.- Subcellular Transcript Localization in Drosophila Embryos and Tissues Visualized by Multiplex FISH.- Application of Alkaline Phosphatase-Mediated Azo Dye Staining for Dual Fluorescent In Situ Hybridization in Zebrafish.- MultiplexFluorescent RNA In Situ Hybridization via RNAscope.- Quantum Dot-Based In Situ Hybridization and Immunohistochemistry to Detect mRNA and Protein at Subcellular Levels, Comparison with Studies under Electron Microscopy.- Quantitative Multiplexed Quantum Dot Based In Situ Hybridisation in Formalin Fixed Paraffin Embedded Tissue.- Single and Multiplexed Fluorescent In Situ Hybridization using Quantum Dots Nanocrystals in Xenopus.- Quantitative Single Molecule mRNA Fluorescent In Situ Hybridization in C. elegans.- In Situ Detection of Individual mRNA Molecules with Padlock Probes and Target-Primed Rolling-Circle Amplification in Fixed Mouse Brain Tissues.- Extended Multiplexed Fluorescent In Situ Hybridisation by Combinatorial Encoding of Individual Transcripts.- Characterizing Cellular Identity at One Cell Resolution.- Transglutaminase-Mediated In Situ Hybridization (TransISH) for mRNA Detection in Mammalian Tissues.- ECHO-FISH for Gene Transcript Detection in Neuronal and Other Cells and Subcellular Compartments.