Since the first edition, published in 2001, genomics research has taken great strides. In Genomics Protocols, 2nd Edition, a team of expert researchers share the most current information in a field that has recently switched emphasis from gene identification to functional genomics and the characterization of genes and gene products. This volume approaches its complex subject with a broad perspective to supply its reader with a vital overview of genomics and its derivative fields, with a focus on pivotal issues such as data analysis. Following the highly successful Methods in Molecular Biology™ series format, the chapters provide easy-to-follow laboratory protocols, lists of the necessary materials, and the excellent Notes section, which offers tips on troubleshooting and avoiding known pitfalls.
Expansive and current, Genomics Protocols, 2nd Edition is the perfect update for researchers working in this integral, growing field.
Table of contents
Contents
Preface
Contributors
1. Whole Genome Amplification with Phi29 DNA Polymerase to enable Genetic or
Genomic Analysis of Samples of Low DNA Yield
Kaisa Silander…………………………………………………………………………
2. Scanning for DNA variants by denaturant capillary electrophoresis
Per O. Ekstrøm………………………………………………………………………..
3. Identification of SNPs, or Mutations in Sequence Chromatograms
Nicole Draper………………………………………………………………………….
4. Beadarray based Genotyping
Helen Butler and Jiannis Ragoussis………………………………………………
5. Microsatellite-Based Candidate Gene Linkage Analysis Studies
Cathryn Mellersh………………………………………………………………...……
6. Full Complexity Genomic Hybridization on 60mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH)
Alexei Protopopov, Bin Feng, and Lynda Chin…………………………………
7. Detection of Copy Number Changes at Multiple Loci in DNA Prepared from
Formalin Fixed, Paraffin-Embedded Tissue by Multiplex Ligation-
Dependent Probe Amplification
Minoru Takata…………………………………………………………………………
8. Application of Microarrays for DNA Methylation Profiling
Axel Schumacher, Andreas Weinhäusl, and Arturas Petronis………………
9. Genome-Wide Identification of Protein Binding Locations using Chromatin Immunoprecipitation coupled with Microarray
Byung-Kwan Cho, Eric M. Knight, and Bernhard Ø. Palsson………………..
10. Transcriptional Profiling of Small Samples in the Central Nervous System
Stephen D. Ginsberg…………………………………………………………………
11. Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-
Embedded Tissues using randomly assembled Bead Arrays
Marina Bibikova, Joanne M. Yeakley, Jessica Wang-Rodriguez,
and Jian-Bing Fan …………………………………………………………………….
12. Expression Profiling of microRNAs in Cancer Cells: Technical Considerations
Mouldy Sioud and Lina Cekaite………………………………………………….…
13. Identification of Disease Biomarkers by Profiling of Serum Proteins using SELDI-TOF Mass Spectrometry
Sigrun Langbein………………………………………………………………………
14. The Applicability of Cluster of Differentiation Monoclonal Antibody Microarrays
to the Diagnosis of Human Disease
Peter Ellmark, Adrian Woolfson, Larissa Belov and Richard I.
Christopherson……………………………………………………………………….
15. Protein Profiling based on Two-Dimensional Difference Gel Electrophoresis
Gert Van den Bergh and Lutgarde Arckens…………………………………….
16. Quantitative protein profiling by mass spectrometry using isotope-coded
affinity tags
Arsalan S. Haqqani, John F. Kelly and Danica B. Stanimirovic……….……
17. Quantitative protein profiling by mass spectrometry using label-free
proteomics
Arsalan S. Haqqani, John F. Kelly and Danica B. Stanimirovic……………
18. Using 2D-LC-MS/MS to identify Francisella tularensis peptides in extracts
from an infected mouse macrophage cell line
John Kelly and Wen Ding…………………………………………………………
19. Baculovirus Expression Vector Systems (BEVS): An Emerging Host for High- Throughput Eukaryotic Protein Expression
Binesh Shrestha, Carol Smee, and Opher Gileadi ………………………….
20. Co-immunoprecipitation and proteomic analyses
S. Fabio Falsone, Bernd Gesslbauer and Andreas J. Kungl………….…..
21. Tandem affinity purification combined with mass spectrometry to identify
components of protein complexes
Peter Kaiser, David Meierhofer, Xiaorong Wang and Lan Huang…………….
22. Mammalian Two-Hybrid Assay For Detecting Protein-Protein Interactions in vivo
Runtao He and Xuguang Li…………………………………………………..……..
23. Detection of Protein-Protein Interactions in Live Cells and Animals with Split
Firefly Luciferase Protein Fragment Complementation
Victor Villalobos, Snehal Naik and David Piwnica-Worms……………………
24. Subcellular Localisation of Intracellular Human Proteins by Construction of
Tagged Fusion Proteins and Transient Expression in COS-7 Cells
John E. Collins…………………………………………………………………….…
25. GeneFAS : A tool for prediction of gene function using multiple sources of
data
Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song and Dong Xu…...…
26. Comparative Genomics-based Prediction of Protein Function
Toni Gabaldón………………………………………………………………..……...
27. Design, Manufacture and Assay of the Efficacy of siRNAs for Gene Silencing
Louise A. Dawson and Badar A. Usmani……………………………….………