Functional Genomics Methods and Protocols

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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 key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing  or extending technologies and techniques in their laboratories.

Part I: Bioinformatics

1. Prediction of Protein Tertiary Structures using MUFOLD

Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, and Dong Xu

2. Prediction of Protein Functions

Roy D. Sleator

3. Genome Wide Screens for Expressed Hypothetical Proteins

Claus Desler, Jon Ambaek Durhuus and Lene Juel Rasmussen

4. Self Custom-Made SFP Arrays for Non-Model Organisms

Ron Ophir and Amir Sherman

Part II: DNA Analysis

5. Construction and Analysis of Full-length and Normalized cDNA Libraries from Citrus

M Carmen Marques and Miguel A Perez-Amador

6. Assembling Linear DNA Templates for In vitro Transcription and Translation

Viktor Stein, Miriam Kaltenbach and Florian Hollfelder

7. Automated Computational Analysis of Genome-wide DNA Methylation Profiling Data from HELP-tagging Assays

Qiang Jing, Andrew McLellan, John M. Greally and Masako Suzuki

Part III: RNA Analysis

8. Detecting of RNA Editing Events in Human Cells using High-Throughput Sequencing

Iouri Chepelev

9. Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization

Ruisheng An and Parwinder S. Grewal

10. Whole Genome RT-qPCR MicroRNA Expression Profiling

Pieter Mestdagh, Stefaan Derveaux, Jo Vandesompele

11. Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG

Siva Kumar Panguluri and Sham S. Kakar

12. FRET-Based Real-Time DNA Microarrays

Arjang Hassibi, Haris Vikalo, José Riechmann and Babak Hassibi

Part IV: Protein Analysis I: Quantification and Indentification

13. 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps

Maria Paola Simula, Agata Notarpietro, Giuseppe Toffoli, and Valli De Re

14. The Use of Antigen Microarrays in Antibody Profiling

Krisztián Papp and József Prechl

15. Limited Proteolysis in Proteomics using Protease-immobilized Microreactors

Hiroshi Yamaguchi, Masaya Miyazaki and Hideaki Maeda

16. Mass Spectrometry for Protein Quantification in Biomarker Discovery

Mu Wang and Jinsam You

Part V: Protein Analysis II: Functional Characterization

17. High-throughput Microtitre Plate-based Assay for DNA Topoisomerases

James A Taylor, Nicolas P Burton and Anthony Maxwell

18. Microscale Thermophoresis as a Sensitive Method to Quantify Protein-Nucleic Acid Interactions in Solutions

Karina Zillner, Moran Jerabek-Willemsen, Stefan Duhr, Dieter Braun, Gernot Längst and Philipp Baaske

19    Bioluminescence Resonance Energy Transfer: an Emerging Tool for the Detection of        Protein-protein Interaction in Living Cells

         Søren W. Gersting, Amelie S. Lotz-Havla and Ania C. Muntau

20    LuMPIS – Luciferase-based MBP-pull-down Protein Interaction Screening System

         María G. Vizoso Pinto and Armin Baiker

21   Yeast Two-Hybrid Screens: Improvement of Array-based Screening Results by N- and   C-terminally Tagged Fusion Proteins

Thorsten Stellberger, Roman Häuser, Peter Uetz, and Albrecht von Brunn

22. Inducible microRNA-mediated Knockdown of the Endogenous Human Lamin A/C Gene

Ina Weidenfeld

23. Multiple-gene Silencing using Antisense RNAs in Escherichia Coli

Nobutaka Nakashima, Shan Goh, Liam Good and Tomohiro Tamura

24. Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and in Situ Hybridization

William Ka Fai Tse and Yun-Jin Jiang

25. Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides

Harris S. Soifer, Troels Koch, Johnathan Lai, Bo Hansen, Anja Hoeg, Henrik Oerum and C.A. Stein

26. Polycistronic Expression of Interfering RNAs and RNA Plymerase III Promoters

Laura F. Steel and Viraj R. Sanghvi

Part VI: Metabolite Analysis

27. Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy

Isvett Josefina Flores-Sanchez, Young Hae Choi and Robert Verpoorte

28. Metabolome Analysis of Grame-positive Bacteria such as Staphylococcus aureus by GC-MS and LC MS

Manuel Liebeke, Kirsten Dörries, Hanna Meyer and Micheal Lalk

29. Metabolic Fingerprinting Using Comprehensive Two-dimensional Gas Chromatography-Time-of-Flight Mass Spectrometry(GCxGX-TOF-MS)

Martin F. Almstetter, Peter J. Oefner, and Katja Dettmer