Functional Genomics: Methods and Protocols

ISBN-13: 9781493972302 / Angielski / Twarda / 2017 / 392 str.

Michael Kaufmann; Claudia Klinger; Andreas Savelsbergh

Spis treści

Part I: Bioinformatics

 

1. Predicting RNA Structure with Vfold

            Chenhan Zhao, Xiaojun Xu, and Shi-Jie Chen

 

2. RNA Function Prediction

            Yongsheng Li, Juan Xu, Tingting Shao, Yunpeng Zhang, Hong Chen, and Xia Li

 

3. Computational Prediction of Novel miRNAs from Genome-Wide Data

            Georgina Stegmayer, Cristian Yones, Laura Kamenetzky, Natalia Macchiaroli, and

Diego H. Milone

 

4. Protein Structure Modeling with MODELLER

            Benjamin Webb and Andrej Sali

 

5. Protein Function Prediction

            Leonardo Magalhães Cruz, Sheyla Trefflich, Vinícius Almir Weiss, and Mauro Antônio Alves Castro

 

Part II: DNA Analysis

 

6. Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C

            Takashi Nagano, Steven W. Wingett, and Peter Fraser

 

7. Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila

            Alexey V. Pindyurin

 

8. DNA Methylation Profiling Using Long-Read Single-Molecule Real-Time Bisulfite Sequencing (SMRT-BS)

            Yao Yang and Stuart A. Scott

 

9. Copy Number Variation Analysis by Droplet Digital PCR

            Suvi K. Härmälä, Robert Butcher, and Chrissy H. Roberts

 

10. MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein-Nucleic Acid Interactions in Solution

            Adrian Michael Müller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, and Gernot Längst

 

11. Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging

            Eric Ehrke-Schulz, Maren Schiwon, Claudia Hagedorn, and Anja Ehrhardt

 

Part III: RNA Analysis

 

12. Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy

            Patrick P. Weil, Yan Jaszczyszyn, Anne Baroin-Tourancheau, Jan Postberg, and Laurence Amar

 

13. MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation

            Alan Van Goethem, Pieter Mestdagh, Tom Van Maerken, and Jo Vandesompele

 

14. Using Firefly^® Particle Technology for Multiplex MicroRNA Profiling Without RNA Purification

            Michael R. Tackett and Izzudin Diwan

 

15. Multiplex Real-Time PCR Using Encoded Microparticles for MicroRNA Profiling

            Seungwon Jung and Sang Kyung Kim

 

16. Optimized Whole Transcriptome Profiling of Motor Axons

            Lena Saal, Michael Briese, and Michael Sendtner

 

Part IV: Protein Analysis

 

17. 2D-DIGE in Proteomics

            Matias Pasquali, Tommaso Serchi, Sebastien Planchon, and Jenny Renaut

 

18. STAGE-Diging in Proteomics

            Paolo Soffientini and Angela Bachi

 

19. Protein Arrays I: Antibody Arrays

            Yulin Yuan, Zuan-Tao Lin, Hongting Wang, Xia Hong, Mikala Heon, and Tianfu Wu

 

20. Protein Arrays II: Antigen Arrays

            Yulin Yuan, Hongting Wang, Zuan-Tao Lin, Xia Hong, Mikala Heon, and Tianfu Wu

 

21. Protein Arrays III: Reverse-Phase Protein Arrays

            Yulin Yuan, Xia Hong, Zuan-Tao Lin, Hongting Wang, Mikala Heon, and Tianfu Wu

 

22. Isolation of Exosomes for the Purpose of Protein Cargo Analysis with the Use of Mass Spectrometry

            Monika Pietrowska, Sonja Funk, Marta Gawin, Łukasz Marczak, Agata Abramowicz, Piotr Widłak, and Theresa Whiteside

 

Part V: From Genotype to Phenotype

 

23. Virus-Induced Gene Silencing (VIGS) and Foreign Gene Expression in Pisum sativum L. Using the ‘One-Step’ Bean pod mottle virus (BPMV) Viral Vector

            Chouaïb Meziadi, Sophie Blanchet, Valérie Geffroy, and Stéphanie Pflieger

 

24. Re-Expressing Epigenetically Silenced Genes by Inducing DNA Demethylation through Targeting of Ten-Eleven Translocation 2 to Any Given Genomic Locus

            Julio Cesar Rendón, David Cano-Rodríguez, and Marianne G. Rots

 

25. Knockdown of Rice MicroRNA166 by Short Tandem Target Mimic (STTM)

            Sachin Teotia, Dabing Zhang, and Guiliang Tang

 

26. RNAi-Mediated Knockdown of Protein Expression

            Volker Baumann, Cornelia Lorenzer, Michael Thell, Anna-Maria Winkler, and Johannes Winkler

 

27. Engineered Zinc Finger DNA-Binding Domains: Synthesis, Assessment of DNA-Binding Affinity, and Direct Protein Delivery to Mammalian Cells

            Mir A. Hossain, Isaac J. Knudson, Shaleen Thakur, Yong Shen, Jared R. Stees, Joeva J. Barrow, and Jörg Bungert

 

28. Production, Purification, and Titration of First-Generation Adenovirus Vectors

            Ramona F. Kratzer and Florian Kreppel

Blurb

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.