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

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.

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