Table of Contents

The Secret Life of RNA: Lessons from Emerging Methodologies.- Quantification of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol).- Identifying the m6A Methylome by Affinity Purification and Sequencing.- PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution.- Axon-TRAP-RiboTag: Affinity-Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo.- LCM-Seq: A Method for Spatial Transcriptomic Profiling using Laser Capture Microdissection Coupled with PolyA-Based RNA Sequencing.- Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas.- Single mRNA Molecule Detection in Drosophila.- Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos.- Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction.- Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections.- Hybridization Chain Reaction for Direct mRNA Detection without Nucleic Acid Purification.- In Situ Detection of MicroRNA Expression with RNAscope Probes.- Padlock Probes to Detect Single Nucleotide Polymorphisms.- Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons.- Optimizing Molecular Beacons for Intracellular Analysis of RNA.- Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH.- In Vivo Visualization and Function Probing of Transport mRNPs using Injected FIT Probes.- Visualizing RNA in Live Bacterial Cells using Fluorophore- and Quencher-Binding Aptamers.- Method for Imaging Live-Cell RNA using an RNA Aptamer and a Fluorescent Probe.- RNA Live Imaging in the Model Microorganism Ustilago maydis.- Real-Time Fluorescence Imaging of Single-Molecule Endogenous Non-Coding RNA in Living Cells.- Live Imaging of mRNA Synthesis in Drosophila.- Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog.- Detection of the First Round of Translation: The TRICK Assay.- Imaging Translation Dynamics of Single mRNA Molecules in Live Cells.- Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding.- Isolation and Characterization of Endogenous RNPs from Brain Tissues.- Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions.- RNA Tagging: Preparation of High-Throughput Sequencing Libraries.- RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells.