DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols
Array Platforms and Wet-Bench Protocols
Academic Press
Published on 19. August 2011
512 pages
978-0-08-046465-7 (ISBN)
Description
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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Additional editions
Alan R. Kimmel | Brian Oliver
DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols: Volume 410
Book
09/2006
Academic Press
€167.13
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Content
Section I. Array PlatformsChapter 1: Getting started with microarraysChapter 2: The Affymetrix GeneChip® Platform: An OverviewChapter 3: The Agilent In-situ-synthesized microarray platformChapter 4: Illumina Universal Bead ArraysChapter 5: Microarray Oligonucleotide-probesChapter 6: Automated liquid handling and high-throughput preparation of PCR amplified DNA for microarray fabricationChapter 7: The Printing Process - Tips on TipsChapter 8: Making and Using Spotted DNA Microarrays in an Academic Core LaboratoryChapter 9: Printing your own Inkjet microarraysChapter 10: Peptide Nucleic Acid (PNA) microarrays made with (S, S)-trans-Cyclopentane-Constrained Peptide Nucleic AcidsSection II. Wet-Bench ProtocolsChapter 11: Good molecular techniqueChapter 12: Optimizing experiment and analysis parameters for spotted microarraysChapter 13: Sample Labeling: An OverviewChapter 14: Genomic DNA as a general cohybridization standard for ratiometric microarraysChapter 15: Analysis of Sequence Specificities of DNA Binding Proteins with Protein Binding MicroarraytChapter 16: Mircroarray analysis of RNA processing and modificationChapter 17: Mapping the distribution of Drosophila chromatin proteins by ChIP on chipChapter 18: DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.Chapter 19: Whole Genome GenotypingChapter 20: Mapping Drosophila Genomic Aberration Breakpoints with Comparative Genome Hybridization On MicroarraysChapter 21: Performing Quantitative RT-PCR ExperimentsChapter 22: The Application of Tissue Microarrays in the Validation of Microarray ResultsChapter 23: Mapping Histone modifications by nucleosome immunoprecipitation
