Oliver DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols

1. Auflage 2011
ISBN: 978-0-08-046465-7
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 410, 512 Seiten, Web PDF

Reihe: Methods in Enzymology

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

Autoren/Hrsg.

Oliver, Brian

Inhaltsverzeichnis

1;Cover Page;1
2;Table of Contents;6
3;Contributors to Volume 410;10
4;Volumes in Series;14
5;Section I Array Platforms;38
5.1;Chapter 1: The Affymetrix GeneChipreg Platform: An Overview;40
5.1.1;Introduction;40
5.1.2;GeneChip Microarrays, a Flexible Platform;42
5.1.3;Array Manufacturing;42
5.1.4;Array Design;45
5.1.5;Target Preparation;50
5.1.6;GeneChip Instrument Components and Associated Assay Steps;54
5.1.7;Image and Data Analysis;55
5.1.8;Current Applications;56
5.1.9;Advancing the Future of Genomics;61
5.1.10;Acknowledgments;61
5.1.11;References;62
5.2;Chapter 2: The Agilent In Situ-Synthesized Microarray Platform;65
5.2.1;Introduction;65
5.2.2;Technology;66
5.2.3;Applications;67
5.2.4;Methods Descriptions;68
5.2.5;Array Design;68
5.2.6;Sample Isolation, Labeling, and Quality Control;69
5.2.7;Array Hybridization and Scanning;70
5.2.8;Data Extraction;71
5.2.9;Array Design;72
5.2.10;Process Description;72
5.2.11;Sample Isolation, Labeling, and Quality Control;74
5.2.12;Array Hybridization and Scanning;79
5.2.13;Data Extraction;84
5.2.14;References;90
5.3;Chapter 3: Illumina Universal Bead Arrays;94
5.3.1;Introduction;95
5.3.2;Material and Methods;95
5.3.3;Results and Discussion;102
5.3.4;Conclusion;107
5.3.5;Acknowledgments;108
5.3.6;References;108
5.4;Chapter 4: Microarray Oligonucleotide Probes;110
5.4.1;The Case for Oligonucleotide Probes;111
5.4.2;Considerations for Oligonucleotide Probe Design;112
5.4.3;Microarray Production and Hybridization Protocols;114
5.4.4;Practical Considerations in Probe Sequence Design, a Case Study;115
5.4.5;Employment and Postprocessing;118
5.4.6;Conclusion;120
5.4.7;Locations of Probe Sequence Target Regions: Discrimination of Highly Similar Targets;120
5.4.8;In Situ Synthesis vs Deposition of Presynthesized Oligonucleotides;122
5.4.9;Thermodynamic Modeling of Microarray Probe Hybridization;123
5.4.10;Outlook;130
5.4.11;Supplement;131
5.4.12;Acknowledgments;131
5.4.13;References;131
5.5;Chapter 5: Automated Liquid Handling and High-Throughput Preparation of Polymerase Chain Reaction-Amplified DNA for Microarray Fabrication;136
5.5.1;Introduction;136
5.5.2;Overview;137
5.5.3;Methods;145
5.5.4;Summary;156
5.5.5;Acknowledgments;157
5.5.6;References;157
5.6;Chapter 6: The Printing Process: Tips on Tips;158
5.6.1;Introduction;158
5.6.2;The Printing Process and Equipment;159
5.6.3;Printing Pin Technology Options;161
5.6.4;Critical Parameters and Troubleshooting;163
5.6.5;Quality Control Testing;168
5.6.6;Future Developments;170
5.6.7;Acknowledgment;171
5.6.8;References;172
5.7;Chapter 7: Making and Using Spotted DNA Microarrays in an Academic Core Laboratory;172
5.7.1;Introduction;173
5.7.2;Technologies and Services Provided by the Keck Microarray Resource;174
5.7.3;Generic Glass Slide Microarray Printing;178
5.7.4;Genomic Solutions OmniGrid 100 Microarrayer Print Settings;179
5.7.5;Materials and General Settings for cDNA and Oligonucleotide Printing on In-House PLL-Coated Slides;180
5.7.6;Quality Control Parameters for DNA Microarray Printing and Analysis Using Spotted Glass Slides;181
5.7.7;Labeling and Hybridization Protocols Employed by the Keck Microarray Resource;183
5.7.8;General Considerations Regarding RNA Samples, Labeling, and Hybridization Strategies;187
5.7.9;Indirect Amino-Allyl dUTP Target Labeling, Monofunctional Dye Conjugation, and cDNA and Oligonucleotide Array Hybridization Protocols;189
5.7.10;Genisphere 3DNA Dendrimer Labeling and Oligonucleotide Array Hybridization;192
5.7.11;Genicon/Invitrogen Resonance Light Scattering Using Gold and Silver Nanoparticle Labeling with HiLight Scanner Detection;196
5.7.12;Scanning and Analyzing Spotted Microarrays;199
5.7.13;Yale Microarray Database;199
5.7.14;Gene Expression Studies Using Keck Microarray Slides and/or Services;202
5.7.15;Acknowledgments;204
5.7.16;References;204
5.8;Chapter 8: Printing Your Own Inkjet Microarrays;205
5.8.1;Introduction;206
5.8.2;Description of Methods;214
5.8.3;Concluding Remarks;223
5.8.4;References;224
5.9;Chapter 9: Peptide Nucleic Acid Microarrays Made with (S,S)-trans-Cyclopentane-Constrained Peptide Nucleic Acids;226
5.9.1;Introduction;226
5.9.2;Experimental Section;228
5.9.3;General Procedure for Manual Solid-Phase Synthesis of Peptide Nucleic Acids;233
5.9.4;Procedure Used to Attach PNA to Surface;236
5.9.5;References;236
6;Section II Wet-Bench Protocols;238
6.1;Chapter 10: Optimizing Experiment and Analysis Parameters for Spotted Microarrays;240
6.1.1;Introduction;240
6.1.2;Factors Affecting the Quality of Experimental Data;241
6.1.3;Factors to Consider in Experimental Design and Analysis;244
6.1.4;Perspectives and Conclusions;255
6.1.5;Acknowledgments;257
6.1.6;References;257
6.2;Chapter 11: Sample Labeling: An Overview;259
6.2.1;Extraction of Nucleic Acids;260
6.2.2;Template Amplification;263
6.2.3;Labeling;266
6.2.4;Conclusions;270
6.2.5;References;271
6.3;Chapter 12: Genomic DNA as a General Cohybridization Standard for Ratiometric Microarrays;274
6.3.1;Introduction;275
6.3.2;Current Cohybridization Standards: RNA;277
6.3.3;DNA Standards;277
6.3.4;Evaluating Cohybridization Standards;278
6.3.5;Recovering Information on RNA Prevalence;278
6.3.6;Shelf Life and Quality Control for Genomic DNA Standards;279
6.3.7;Method;280
6.3.8;Equipment and Reagents;282
6.3.9;Freezing and Pulverization;283
6.3.10;Tissue Lysis;283
6.3.11;Protein Precipitation;284
6.3.12;Genomic DNA Precipitation and Resuspension;284
6.3.13;RNase Digestion;285
6.3.14;Sonication;285
6.3.15;Column Cleanup;285
6.3.16;Labeling Method I. Direct Incorporation of Cy-Labeled dCTP;286
6.3.17;Equipment and Reagents;287
6.3.18;Labeling;288
6.3.19;Cleanup;289
6.3.20;Prepare the Labeled Target for the Array;289
6.3.21;Fluorometric Quantification of Reaction Yield and Label Incorporation;290
6.3.22;Equipment and Reagents;290
6.3.23;Quantifying Yield and Incorporation Efficiency;290
6.3.24;Labeling Method II. Indirect Labeling via Incorporation of Amino-allyl dUTP;291
6.3.25;Equipment and Reagents;293
6.3.26;Protocol for Resuspension of Dry Cy Dye in DMSO;294
6.3.27;10x Aminoallyl-dUTP/dNTPS Labeling Mix;295
6.3.28;Denature Sonicated Genomic DNA Template with NaOH;295
6.3.29;Cleanup over Zymo Columns (either 5 or 25 mug Capacity);295
6.3.30;Annealing to Random Primers;296
6.3.31;Labeling;296
6.3.32;Cleanup;297
6.3.33;Coupling to Monofunctional Reactive Dye;297
6.3.34;Qiagen PCR Column to Remove Enzyme and Uncoupled Dye from Sample;298
6.3.35;Final Cleanup over P30 Biogel Chromatography Column;298
6.3.36;Prepare the Labeled Target for the Array;299
6.3.37;Quantifying Yield and Incorporation Efficiency;299
6.3.38;Conclusions;310
6.3.39;Acknowledgments;313
6.3.40;References;313
6.4;Chapter 13: Analysis of Sequence Specificities of DNA-Binding Proteins with Protein Binding Microarrays;316
6.4.1;Introduction;316
6.4.2;Preparation of DNA Microarrays for Use in Protein Binding Microarray Experiments;320
6.4.3;Protein Binding Microarray Experiments;324
6.4.4;Analysis of Protein Binding Microarray Data;328
6.4.5;Conclusions;334
6.4.6;Acknowledgments;335
6.4.7;References;335
6.5;Chapter 14: Microarray Analysis of RNA Processing and Modification;337
6.5.1;Introduction;337
6.5.2;Microarrays for Measuring Noncoding RNA Processing and Modification;338
6.5.3;Microarrays for Covalent RNA Modification;344
6.5.4;Microarrays for Monitoring Alternative Splicing;344
6.5.5;Alternative Splicing Microarray Design;347
6.5.6;Conclusion;351
6.5.7;Acknowledgments;351
6.5.8;References;351
6.6;Chapter 15: Mapping the Distribution of Chromatin Proteins by ChIP on Chip;353
6.6.1;Introduction;354
6.6.2;Chromatin Immunoprecipitation;356
6.6.3;Chips for ChIPs;362
6.6.4;Labeling and Hybridization;366
6.6.5;Data Acquisition;368
6.6.6;Statistical Analysis of Data;370
6.6.7;Graphic Comparison of ChIP on Chip Data with Genome Annotations;374
6.6.8;Perspectives;375
6.6.9;Acknowledgments;375
6.6.10;References;376
6.7;Chapter 16: DamID: Mapping of In Vivo Protein-Genome Interactions Using Tethered DNA Adenine Methyltransferase;379
6.7.1;Introduction;379
6.7.2;Principle of DamID;380
6.7.3;Correcting for Untargeted Binding of Dam;381
6.7.4;Expression Levels of Dam and Dam Fusion Proteins;382
6.7.5;Comparison of DamID and ChIP;384
6.7.6;Materials;385
6.7.7;Methods;387
6.7.8;Acknowledgments;395
6.7.9;References;395
6.8;Chapter 17: Whole-Genome Genotyping;396
6.8.1;Introduction;397
6.8.2;Methods;405
6.8.3;Conclusions;411
6.8.4;Acknowledgments;412
6.8.5;References;412
6.9;Chapter 18: Mapping Drosophila Genomic Aberration Breakpoints with Comparative Genome Hybridization on Microarrays;414
6.9.1;Introduction;414
6.9.2;Materials and Methods;417
6.9.3;Acknowledgments;422
6.9.4;References;422
6.10;Chapter 19: Performing Quantitative Reverse-Transcribed Polymerase Chain Reaction Experiments;423
6.10.1;Introduction;424
6.10.2;Choice of the Fluorescence Format;425
6.10.3;Choice of the Enzymatic System;425
6.10.4;Amplification and Denaturation Curves;426
6.10.5;Determination of the Correct Annealing Temperature: Specificity;429
6.10.6;Checking the Amplification Yield: Efficiency;429
6.10.7;Relative Quantification;432
6.10.8;Multiplex Polymerase Chain Reaction;434
6.10.9;Proposed Reaction Medium for SYBR Green Q-PCR;434
6.10.10;Conclusion;435
6.10.11;References;436
6.11;Chapter 20: The Application of Tissue Microarrays in the Validation of Microarray Results;437
6.11.1;Introduction;437
6.11.2;Ethical Concerns in the Use of Tissue in Biomedical Research;439
6.11.3;Determining What Tissue to Analyze;440
6.11.4;Construction of a Tissue Microarray;441
6.11.5;Obtaining a Tissue Microarray from Other Sources;443
6.11.6;Confirmation, Validation, and Determining Experimental Approach;444
6.11.7;Immunohistochemical Assays for Validation;445
6.11.8;In Situ Assays;447
6.11.9;Collection and Interpretation of Data;448
6.11.10;Analysis of Data;449
6.11.11;Other Applications of TMAs Relating to Microarrays;450
6.11.12;Conclusions;451
6.11.13;References;451
6.12;Chapter 21: Mapping Histone Modifications by Nucleosome Immunoprecipitation;453
6.12.1;Introduction;453
6.12.2;Preparation of Core Particles: MNase Digestion of Minichromosomes;455
6.12.3;Immunoprecipitation of Nucleosomes;457
6.12.4;Radioactive End Labeling of Nucleosome Core Particle DNA;458
6.12.5;Analysis of Immunoprecipitated Nucleosomes;458
6.12.6;Alkali Denaturation of Immunoprecipitated, Labeled Core Particle DNA;462
6.12.7;Monomer Extension;462
6.12.8;Analysis of the Histone Modification Map;464
6.12.9;Concluding Remarks;465
6.12.10;Acknowledgments;466
6.12.11;References;466
7;Author Index;468
8;Subject Index;498