Functional Genomics: Methods and Protocols

Front Matter ....Pages i-xv
Front Matter ....Pages 1-1
 Predicting RNA Structure with Vfold  (Chenhan Zhao, Xiaojun Xu, Shi-Jie Chen)....Pages 3-15
 RNA Function Prediction  (Yongsheng Li, Juan Xu, Tingting Shao, Yunpeng Zhang, Hong Chen, Xia Li)....Pages 17-28
 Computational Prediction of Novel miRNAs from Genome-Wide Data  (Georgina Stegmayer, Cristian Yones, Laura Kamenetzky, Natalia Macchiaroli, Diego H. Milone)....Pages 29-37
 Protein Structure Modeling with MODELLER  (Benjamin Webb, Andrej Sali)....Pages 39-54
 Protein Function Prediction  (Leonardo Magalhães Cruz, Sheyla Trefflich, Vinícius Almir Weiss, Mauro Antônio Alves Castro)....Pages 55-75
Front Matter ....Pages 77-77
 Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C  (Takashi Nagano, Steven W. Wingett, Peter Fraser)....Pages 79-97
 Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila  (Alexey V. Pindyurin)....Pages 99-124
 DNA Methylation Profiling Using Long-Read Single Molecule Real-Time Bisulfite Sequencing (SMRT-BS)  (Yao Yang, Stuart A. Scott)....Pages 125-134
 Copy Number Variation Analysis by Droplet Digital PCR  (Suvi K. Härmälä, Robert Butcher, Chrissy H. Roberts)....Pages 135-149
 MicroScale Thermophoresis: A Rapid and Precise Method to Quantify Protein–Nucleic Acid Interactions in Solution  (Adrian Michael Mueller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, Gernot Längst)....Pages 151-164
 Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging  (Eric Ehrke-Schulz, Maren Schiwon, Claudia Hagedorn, Anja Ehrhardt)....Pages 165-176
Front Matter ....Pages 177-177
 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, Laurence Amar)....Pages 179-196
 MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation  (Alan Van Goethem, Pieter Mestdagh, Tom Van Maerken, Jo Vandesompele)....Pages 197-208
 Using FirePlex™ Particle Technology for Multiplex MicroRNA Profiling Without RNA Purification  (Michael R. Tackett, Izzuddin Diwan)....Pages 209-219
 Multiplex Real-Time PCR Using Encoded Microparticles for MicroRNA Profiling  (Seungwon Jung, Sang Kyung Kim)....Pages 221-230
 Optimized Whole Transcriptome Profiling of Motor Axons  (Lena Saal-Bauernschubert, Michael Briese, Michael Sendtner)....Pages 231-241
Front Matter ....Pages 243-243
 2D-DIGE in Proteomics  (Matias Pasquali, Tommaso Serchi, Sebastien Planchon, Jenny Renaut)....Pages 245-254
 STAGE-Diging in Proteomics  (Paolo Soffientini, Angela Bachi)....Pages 255-260
 Protein Arrays I: Antibody Arrays  (Yulin Yuan, Zuan-Tao Lin, Hongting Wang, Xia Hong, Mikala Heon, Tianfu Wu)....Pages 261-269
 Protein Arrays II: Antigen Arrays  (Yulin Yuan, Hongting Wang, Zuan-Tao Lin, Xia Hong, Mikala Heon, Tianfu Wu)....Pages 271-277
 Protein Arrays III: Reverse-Phase Protein Arrays  (Yulin Yuan, Xia Hong, Zuan-Tao Lin, Hongting Wang, Mikala Heon, Tianfu Wu)....Pages 279-289
 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 et al.)....Pages 291-307
Front Matter ....Pages 309-309
 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, Stéphanie Pflieger)....Pages 311-319
 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, Marianne G. Rots)....Pages 321-335
 Knockdown of Rice microRNA166 by Short Tandem Target Mimic (STTM)  (Sachin Teotia, Dabing Zhang, Guiliang Tang)....Pages 337-349
 RNAi-Mediated Knockdown of Protein Expression  (Volker Baumann, Cornelia Lorenzer, Michael Thell, Anna-Maria Winkler, Johannes Winkler)....Pages 351-360
 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 et al.)....Pages 361-375
 Production, Purification, and Titration of First-Generation Adenovirus Vectors  (Ramona F. Kratzer, Florian Kreppel)....Pages 377-388
Back Matter ....Pages 389-392