RNA Abundance Analysis: Methods and Protocols

ISBN-13: 9781617798382 / Angielski / Twarda / 2012 / 231 str.

Hailing Jin; Walter Gassmann

Opis

RNA abundance analysis is one of the most important approaches for gene expression studies in the field of molecular biology. In RNA Abundance Analysis: Methods and Protocols, expert researchers cover 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. This volume includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, sulfur-containing RNAs, viral and satellite RNAs, RNA isoforms, and alternatively spliced RNA variants from various organisms, as well as key discussions of computational data processing for genome-wide datasets. 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. Essential and easy to use, RNA Abundance Analysis: Methods and Protocols provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and modified RNAs, which can assist you in your gene expression studies.

Spis treści

1. SuperSAGE: Powerful Serial Analysis of Gene Expression

            Hideo Matsumura, Naoya Urasaki, Kentaro Yoshida, Detlev H. Krüger, Günter Kahl, and Ryohei Terauchi

 

2. Northern Blot Analysis for Expression Profiling of mRNAs and Small RNAs

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

 

3. Construction of RNA-Seq Libraries from Large and Microscopic Tissues for the Illumina Sequencing Platform

            Hagop S. Atamian and Isgouhi Kaloshian

 

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

            Nadia Ponts, Duk-Won D. Chung, and Karine G. Le Roch

 

5. RNA In Situ Hybridization in Arabidopsis

            Miin-Feng Wu and Doris Wagner

 

6. Laser Microdissection of Cells and Isolation of High-Quality RNA After Cryosectioning

            Marta Barcala, Carmen Fenoll, and Carolina Escobar

 

7. Detection and Quantification of Alternative Splicing Variants Using RNA-Seq

            Douglas W. Bryant, Jr., Henry D. Priest, and Todd C. Mockler

 

8. Separating and Analyzing Sulfur-Containing RNAs with Organomercury Gels

            Elisa Biondi and Donald H. Burke

 

9. RNAse Mapping and Quantitation of RNA Isoforms

            Lakshminarayan K. Venkatesh, Olufemi Fasina, and David J. Pintel

 

10. Detection and Quantification of Viral and Satellite RNAs in Plant Hosts

            Sun-Jung Kwon, Jang-Kyun Seo, and A.L.N. Rao

 

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

            Xiaozhen Yao, Hai Huang, and Lin Xu

 

12. Small RNA Isolation and Library Construction for Expression Profiling of Small RNAs from Neurospora and Fusarium Using Illumina High Throughput Deep Sequencing

            Gyungsoon Park and Katherine A. Borkovich

 

13. Isolation and Profiling of Protein-Associated Small RNAs

            Hongwei Zhao, Yifan Lii, Pei Zhu, and Hailing Jin

 

14. New Virus Discovery by Deep Sequencing of Small RNAs

            Kashmir Singh, Ravneet Kaur, and Wenping Qiu

 

15. Global Assembly of Expressed Sequence Tags (ESTs)

            Foo Cheung

 

16. Computational Analysis of RNA-Seq

            Scott A. Givan, Christopher A. Bottoms, and William G. Spollen

 

17. 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