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DNA microarrays
Title
DNA microarrays / edited by Alan Kimmel & Brian Oliver.
ISBN
9780080464657
0080464653
9780121828158
0121828158
9780121828165
0121828166
Published
Amsterdam ; San Diego : Elsevier/Academic Press, ©2006.
Physical Description
1 online resource (2 volumes) : illustrations.
Local Notes
Access is available to the Yale community.
Access and use
Access restricted by licensing agreement.
Summary
Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results. Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations. Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician. Provides an overview of platforms Includes experimental design and wet bench protocols Presents statistical and data analysis methods, array databases, data visualization and meta analysis.
Variant and related titles
Elsevier ScienceDirect All Books. OCLC KB.
Other formats
Print version: DNA microarrays. Amsterdam ; Boston : Elsevier/Academic Press, ©2006-
Format
Books / Online
Language
English
Added to Catalog
May 17, 2018
Series
Methods in enzymology, v. 410- 411
Bibliography
Includes bibliographical references and indexes.
Contents
pt. A. Array platforms and wet-bench protocols
pt. B. Databases and statistics.
Section I Array Platforms
Chapter 1: The Affymetrix GeneChipreg Platform: An Overview
Introduction
GeneChip Microarrays, a Flexible Platform
Array Manufacturing
Array Design
Target Preparation
GeneChip Instrument Components and Associated Assay Steps
Image and Data Analysis
Current Applications
Advancing the Future of Genomics
Acknowledgments
References
Chapter 2: The Agilent In Situ-Synthesized Microarray Platform
Introduction
Technology
Applications
Methods Descriptions
Array Design
Sample Isolation, Labeling, and Quality Control
Array Hybridization and Scanning
Data Extraction
Array Design
Process Description
Sample Isolation, Labeling, and Quality Control
Array Hybridization and Scanning
Data Extraction
References
Chapter 3: Illumina Universal Bead Arrays
Introduction
Material and Methods
Results and Discussion
Conclusion
Acknowledgments
References
Chapter 4: Microarray Oligonucleotide Probes
The Case for Oligonucleotide Probes
Considerations for Oligonucleotide Probe Design
Microarray Production and Hybridization Protocols
Practical Considerations in Probe Sequence Design, a Case Study
Employment and Postprocessing
Conclusion
Locations of Probe Sequence Target Regions: Discrimination of Highly Similar Targets
In Situ Synthesis vs Deposition of Presynthesized Oligonucleotides
Thermodynamic Modeling of Microarray Probe Hybridization
Outlook
Supplement
Acknowledgments
References
Chapter 5: Automated Liquid Handling and High-Throughput Preparation of Polymerase Chain Reaction-Amplified DNA for Microarray Fabrication
Introduction
Overview
Methods
Summary
Acknowledgments
References
Chapter 6: The Printing Process: Tips on Tips
Introduction
The Printing Process and Equipment
Printing Pin Technology Options
Critical Parameters and Troubleshooting
Quality Control Testing
Future Developments
Acknowledgment
References
Chapter 7: Making and Using Spotted DNA Microarrays in an Academic Core Laboratory
Introduction
Technologies and Services Provided by the Keck Microarray Resource
Generic Glass Slide Microarray Printing
Genomic Solutions OmniGrid 100 Microarrayer Print Settings
Materials and General Settings for cDNA and Oligonucleotide Printing on In-House PLL-Coated Slides
Quality Control Parameters for DNA Microarray Printing and Analysis Using Spotted Glass Slides
Labeling and Hybridization Protocols Employed by the Keck Microarray Resource
General Considerations Regarding RNA Samples, Labeling, and Hybridization Strategies
Indirect Amino-Allyl dUTP Target Labeling, Monofunctional Dye Conjugation, and cDNA and Oligonucleotide Array Hybridization Protocols
Genisphere 3DNA Dendrimer Labeling and Oligonucleotide Array Hybridization
tidtid6.
Subjects
Subjects (Medical)
Oligonucleotide Array Sequence Analysis - methods.
DNA.
Gene Expression Profiling - methods.
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