Functional Genomics: Methods and Protocols

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

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)

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

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

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, Lukasz Marczak, Agata Abramowicz, Piotr Widlak, 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

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