DNA Microarrays Part A: Array Platforms & Wet-Bench Protocols
Alan Kimmel and Brian Oliver
Edited by Alan Kimmel and Brian Oliver
See also Part B
Hardback 512 pp ISBN 9780121828158
- 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 r
eproducibly 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.
Of interest to biochemists and related researchers working with DNA microarray technologies.
Section I. Array Platforms.
- Getting started with microarrays.
- The Affymetrix GeneChip (Registered) Platform: An Overview.
- The Agilent In-situ-synthesized microarray platform.
- Illumina Universal Bead Arrays.
- Microarray Oligonucleotide-probes.
- Automated liquid handling and high-throughput preparation of PCR amplified DNA for microarray fabrication.
- The Printing Process - Tips on Tips.
- Making and Using Spotted DNA Microarrays in an Academic Core Laboratory.
- Printing your own Inkjet microarrays.
- Peptide Nucleic Acid (PNA) microarrays made with (S, S)-trans-Cyclopentane-Constrained Peptide Nucleic Acids.
Section II. Wet-Bench Protocols.
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: analytical methods