· 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
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.
Biochemists and related researchers working with DNA microarray technologies.
DNA Microarrays Part A: Array Platforms & Wet-Bench Protocols, 1st Edition
Section I. Array Platforms.
Chapter 1: Getting started with microarrays.
Chapter 2: The Affymetrix GeneChip® Platform: An Overview.
Chapter 3: The Agilent In-situ-synthesized microarray platform.
Chapter 4: Illumina Universal Bead Arrays.
Chapter 5: Microarray Oligonucleotide-probes.
Chapter 6: Automated liquid handling and high-throughput preparation of PCR amplified DNA for microarray fabrication.
Chapter 7: The Printing Process – Tips on Tips.
Chapter 8: Making and Using Spotted DNA Microarrays in an Academic Core Laboratory.
Chapter 9: Printing your own Inkjet microarrays.
Chapter 10: Peptide Nucleic Acid (PNA) microarrays made with (S, S)-trans-Cyclopentane-Constrained Peptide Nucleic Acids.
Section II. Wet-Bench Protocols.
Chapter 11: Good molecular technique.
Chapter 12: Optimizing experiment and analysis parameters for spotted microarrays.
Chapter 13: Sample Labeling: An Overview.
Chapter 14: Genomic DNA as a general cohybridization standard for ratiometric microarrays.
Chapter 15: Analysis of Sequence Specificities of DNA Binding Proteins with Protein Binding Microarrayt.
Chapter 16: Mircroarray analysis of RNA processing and modification.
Chapter 17: Mapping the distribution of Drosophila chromatin proteins by ChIP on chip.
Chapter 18: DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase.
Chapter 19: Whole Genome Genotyping.
Chapter 20: Mapping Drosophila Genomic Aberration Breakpoints with Comparative Genome Hybridization On Microarrays.
Chapter 21: Performing Quantitative RT-PCR Experiments.
Chapter 22: The Application of Tissue Microarrays in the Validation of Microarray Results.
Chapter 23: Mapping Histone modifications by nucleosome immunoprecipitation.