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This updated book covers a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches. It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms. RNA editing and the computational data processing for genome-wide datasets is also discussed. Written for the highly successful Methods in Molecular Biology series, 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.
Authoritative and practical, RNA Abundance Analysis: Methods and Protocols, Second Edition provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and other RNA variants, in order to assist researchers in their gene expression studies.
List of contents
CRISPR-Cas RNA Targeting Using Transient Cas13a Expression in Nicotiana benthamiana.- Strand-Specific RNA-Seq Applied to Malaria Samples.- Laser Microdissection of Cells and Isolation of High-Quality RNA after Cryosectioning.- Detection of RNA in Ribonucleoprotein Complexes by Blue Native Northern Blotting.- Quantitative Analysis of Plant miRNA Primary Transcripts.- A Revised Adaptation of the Smart-Seq2 Protocol for Single Nematode RNA-Seq.- Analysis of RBP Regulation and Co-Regulation of mRNA 3' UTR Regions in a Luciferase Reporter System.- Extraction of Small RNAs by Titanium Dioxide Nanofibers.- Identification of MicroRNAs and Natural Antisense Transcript-Originated Endogenous siRNAs from Small-RNA Deep Sequencing Data.- Purification and Analysis of Chloroplast RNAs in Arabidopsis.- In Situ Detection of Mature miRNAs in Plants Using LNA-Modified DNA Probes.- Northern Blotting Technique for Detection and Expression Analysis of mRNAs and Small RNAs.- Isolation of Insect Bacteriocytes as a Platform for Transcriptomic Analyses.- Small RNA Isolation and Library Construction for Expression Profiling of Small RNAs from Neurospora crassa and Fusarium oxysporum and Analysis of Small RNAs in Fusarium oxysporum-Infected Plant Root Tissue.- Studying RNA-Protein Interaction Using Riboproteomics.- Small RNA Extraction and Quantification of Isolated Fungal Cells from Plant Tissue by the Sequential Protoplastation.
