RNA Abundance Analysis Methods and Protocols

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. 

1. CRISPR-Cas RNA Targeting Using Transient Cas13a Expression in Nicotiana benthamiana

            Veerendra Sharma, Wenguang Zheng, Jun Huang, and David E. Cook

 

2. Strand-Specific RNA-Seq Applied to Malaria Samples

            Xueqing Maggie Lu and Karine Le Roch

 

3. Laser Microdissection of Cells and Isolation of High-Quality RNA after Cryosectioning

            Marta Barcala, Carmen Fenoll, and Carolina Escobar

 

4. Detection of RNA in Ribonucleoprotein Complexes by Blue Native Northern Blotting

            Lena Krüßel, Steffen Ostendorp, Anna Ostendorp, and Julia Kehr

 

5. Quantitative Analysis of Plant miRNA Primary Transcripts

            Jakub Dolata, Andrzej Zielezinski, Agata Stepien, Katarzyna Kruszka, Dawid Bielewicz, Andrzej Pacak, Artur Jarmolowski, Wojciech Karlowski, and Zofia Szweykowska-Kulinska

 

6. A Revised Adaptation of the Smart-Seq2 Protocol for Single Nematode RNA-Seq

            Dennis Chang, Lorrayne Serra, Dihong Lu, Ali Mortazavi, and Adler Dillman

 

7. Analysis of RBP Regulation and Co-Regulation of mRNA 3’ UTR Regions in a Luciferase Reporter System

            Erin L. Sternburg and Fedor V. Karginov

 

8. Extraction of Small RNAs by Titanium Dioxide Nanofibers

            Luis A. Jimenez and Wenwan Zhong

 

9. Identification of MicroRNAs and Natural Antisense Transcript-Originated Endogenous siRNAs from Small-RNA Deep Sequencing Data

            Weixiong Zhang, Xuefeng Zhou, Xiang Zhou, and Jing Xia

 

10. Purification and Analysis of Chloroplast RNAs in Arabidopsis

            Huan Wang and Hailing Jin

 

11. In Situ Detection of Mature miRNAs in Plants Using LNA-Modified DNA Probes

            Xiaozhen Yao, Hai Huang, and Lin Xu

 

12. Northern Blotting Technique for Detection and Expression Analysis of mRNAs and Small RNAs

            Ankur R. Bhardwaj, Ritu Pandey, Manu Agarwal, and Surekha Katiyar-Agarwal

 

13. Isolation of Insect Bacteriocytes as a Platform for Transcriptomic Analyses

            Mélanie Ribeiro Lopes, Pierre Simonet, Gabrielle Duport, Karen Gaget, Séverine Balmand, Akiko Sugio, Jean-Christophe Simon, Nicolas Parisot, and Federica Calevro

 

14. 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, and Katherine A. Borkovich

 

15. Studying RNA-Protein Interaction Using Riboproteomics

            Sonali Chaturvedi and A.L.N. Rao

 

16. Small RNA Extraction and Quantification of Isolated Fungal Cells from Plant Tissue by the Sequential Protoplastation

            Qiang Cai and Hailing Jin