RNA Abundance Analysis : Methods and Protocols

✍ Scribed by Hailing Jin, Isgouhi Kaloshian

• Publisher: Springer US;Humana
• Year: 2021
• Tongue: English
• Leaves: 235
• Series: Methods in Molecular Biology 2170
• Edition: 2nd ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
CRISPR-Cas RNA Targeting Using Transient Cas13a Expression in Nicotiana benthamiana (Veerendra Sharma, Wenguang Zheng, Jun Huang, David E. Cook)....Pages 1-18
Strand-Specific RNA-Seq Applied to Malaria Samples (Xueqing Maggie Lu, Karine Le Roch)....Pages 19-33
Laser Microdissection of Cells and Isolation of High-Quality RNA After Cryosectioning (Marta Barcala, Carmen Fenoll, Carolina Escobar)....Pages 35-43
Detection of RNA in Ribonucleoprotein Complexes by Blue Native Northern Blotting (Lena Krüßel, Steffen Ostendorp, Anna Ostendorp, Julia Kehr)....Pages 45-51
Quantitative Analysis of Plant miRNA Primary Transcripts (Jakub Dolata, Andrzej Zielezinski, Agata Stepien, Katarzyna Kruszka, Dawid Bielewicz, Andrzej Pacak et al.)....Pages 53-77
A Revised Adaptation of the Smart-Seq2 Protocol for Single-Nematode RNA-Seq (Dennis Chang, Lorrayne Serra, Dihong Lu, Ali Mortazavi, Adler Dillman)....Pages 79-99
Analysis of RBP Regulation and Co-regulation of mRNA 3′ UTR Regions in a Luciferase Reporter System (Erin L. Sternburg, Fedor V. Karginov)....Pages 101-115
Extraction of Small RNAs by Titanium Dioxide Nanofibers (Luis A. Jimenez, Wenwan Zhong)....Pages 117-124
Identification of MicroRNAs and Natural Antisense Transcript-Originated Endogenous siRNAs from Small-RNADeep Sequencing Data (Weixiong Zhang, Xuefeng Zhou, Xiang Zhou, Jing Xia)....Pages 125-131
Purification and Analysis of Chloroplast RNAs in Arabidopsis (Huan Wang, Hailing Jin)....Pages 133-141
In Situ Detection of Mature miRNAs in Plants Using LNA-Modified DNA Probes (Xiaozhen Yao, Hai Huang, Lin Xu)....Pages 143-154
Northern Blotting Technique for Detection and Expression Analysis of mRNAs and Small RNAs (Ankur R. Bhardwaj, Ritu Pandey, Manu Agarwal, Surekha Katiyar-Agarwal)....Pages 155-183
Isolation of InsectBacteriocytes as a Platform for Transcriptomic Analyses (Mélanie Ribeiro Lopes, Pierre Simonet, Gabrielle Duport, Karen Gaget, Séverine Balmand, Akiko Sugio et al.)....Pages 185-198
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 (Shou-Qiang Ouyang, Gyungsoon Park, Hui-Min Ji, Katherine A. Borkovich)....Pages 199-212
Studying RNA–Protein Interaction Using Riboproteomics (Sonali Chaturvedi, A. L. N. Rao)....Pages 213-218
Small RNA Extraction and Quantification of Isolated Fungal Cells from Plant Tissue by the Sequential Protoplastation (Qiang Cai, Hailing Jin)....Pages 219-229
Back Matter ....Pages 231-233

✦ Subjects

Life Sciences; Biochemistry, general; Biological Techniques