Functional Genomics Methods and Protocols

Reflecting developments in genome editing, this third edition volume fully updates a collection of key techniques for the study of functional genomics. The book is broken up into sections on bioinformatics, DNA, RNA, and protein analysis, as well as a closing section entitled “From Genotype to Phenotype.” 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.

Updated and authoritative, Functional Genomics: Methods and Protocols, Third Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

Predicting RNA Structure with Vfold.- RNA Function Prediction.- Computational Prediction of Novel miRNAs from Genome-Wide Data.- Protein Structure Modeling with MODELLER.- Protein Function Prediction.- Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C.- Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila.- DNA Methylation Profiling Using Long-Read Single-Molecule Real-Time Bisulfite Sequencing (SMRT-BS).- Copy Number Variation Analysis by Droplet Digital PCR.- MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution.- Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging.- Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy.- MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation.- Using Firefly^® Particle Technology for Multiplex MicroRNA Profiling Without RNA Purification.- Multiplex Real-Time PCR Using Encoded Microparticles for MicroRNA Profiling.- Optimized Whole Transcriptome Profiling of Motor Axons.- 2D-DIGE in Proteomics.- STAGE-Diging in Proteomics.- Protein Arrays I: Antibody Arrays.- Protein Arrays II: Antigen Arrays.- Protein Arrays III: Reverse-Phase Protein Arrays.- Isolation of Exosomes for the Purpose of Protein Cargo Analysis with the Use of Mass Spectrometry.- Virus-Induced Gene Silencing (VIGS) and Foreign Gene Expression in Pisum sativum L. Using the ‘One-Step’ Bean pod mottle virus (BPMV) Viral Vector.- Re-Expressing Epigenetically Silenced Genes by Inducing DNA Demethylation through Targeting of Ten-Eleven Translocation 2 to Any Given Genomic Locus.- Knockdown of Rice MicroRNA166 by Short Tandem Target Mimic (STTM).- RNAi-Mediated Knockdown of Protein Expression.- Engineered Zinc Finger DNA-Binding Domains: Synthesis, Assessment of DNA-Binding Affinity, and Direct Protein Delivery to Mammalian Cells.- Production, Purification, and Titration of First-Generation Adenovirus Vectors.