DNA microarrays / edited by Alan Kimmel & Brian Oliver.

Contributor(s): Kimmel, Alan R [editor.] | Oliver, Brian, 1959- [editor.]
Material type: TextTextSeries: Methods in enzymology: v. 410.; Methods in enzymology: v. 411.Publisher: San Diego, California : Elsevier/Academic Press, ©2006Description: 1 online resource (parts A-B) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9780080464657; 0080464653Subject(s): DNA microarrays | DNA | Oligonucleotide Array Sequence Analysis -- methods | DNA | Gene Expression Profiling -- methods | DNA | DNA microarrays | dna | dna libraries | dna probes | genexpressie | gene expression | rna | Nucleic AcidsGenre/Form: Electronic books. Additional physical formats: Print version:: DNA microarrays.DDC classification: 572.8636 LOC classification: QP601 | .C733Online resources: Click here to access online
Contents:
Array platforms and wet-bench protocols -- 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.
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.
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Includes bibliographical references and indexes.

Part A (v. 410) Array platforms and wet-bench protocols -- Part B (v. 411) 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.

Print version record.

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.

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