DNA Microarrays for Biomedical Research

Initially an application for mRNA, DNA microarray technology is now used for many applications, some from large commercial providers. This book explores those applications and includes details to design and produce one's own probes and arrays.

DNA microarray technology has revolutionized research in the past decade. Initially an application for mRNA expression studies, the technology now has spread to other applications such as comparative genomic hybridization, SNP and mutation analysis. In DNA Microarrays for Biomedical Research: Methods and Protocols, experts explore these now commonly used applications, addressing probe design strategies, fabrication issues and providing practical examples of detailed methods for generation of high quality DNA microarray data. Chapters incorporate information on some of the largest providers of microarray, including Affymetrix, Ilumina and Agilent, and their use on a variety of applications. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls.

Authoritative and highly practical, DNA Microarrays for Biomedical Research: Methods and Protocols presents a variety of protocols which can be easily reproduced, allowing researchers to gain surprising insight into the complex world of DNA microarray technology.

Covers the use of DNA array from the largest commercial providers

Includes practical details to design and produce your own probes and arrays

Provides methods for gene expression profiling, SNP mutation analysis, comparative genomic hybridization, resequencing, and ChIP on chip assays

Includes supplementary material: sn.pub/extras

Inhalt
DNA Microarrays for Biomedical Research Table of contents Preface Contributors 1. Introduction to microarray technology Martin Dufva 2. Probe design for expression arrays using Oligowiz Rasmus Wernersson 3. Comparative genomic hybridization: microarray design and data interpretation Richard Redon and Nigel P Carter 4. Design of tag SNP whole genome genotyping arrays Daniel A. Peiffer and Kevin L Gunderson 5. Fabrication of DNA microarray Martin Dufva 6. Immobilization chemistries Sascha Todt and Dietmar H Blohm 7. Fabrication using contact spotter Annelie Waldén and Peter Nilsson 8. RNA preparation and characterization for gene expression studies Michael Stangegaard 9. Gene expression analysis using Agilent DNA microarrays Michael Stangegaard 10. Target preparation for genotyping specific genes or gene segments Jesper Petersen, Lena Poulsen and Martin Dufva 11. Genotyping of mutations in the beta-globin gene using allele specific hybridization. Lena Poulsen, Jesper Petersen and Martin Dufva 12. Microarray temperature optimization using hybridization kinetics. Steve Blair, Layne Williams, Justin Bishop, Alexander Chagovetz 13. Whole-Genome Genotyping on bead arrays Kevin L Gunderson 14. Genotyping single nucleotide poymorphosms by multiplex minisequencing using Tag arrays Lili Milani and Ann-Christine Syvänen 15. Resequencing arrays for diagnostics of respiratory pathogens Baochuan Lin and Anthony P Malanoski 16. Comparative genomic hybridization: DNA preparation for microarray fabrication Richard Redon, Diane Riglerand Nigel P Charter 17. Comparative genomic hybridization: DNA labelling, hybridization and detection Richard Redon, Tomas Fitzgerald and Nigel P Charter 18. Chromatin immuno-precipitation using microarrays Michaël Durand-Dubief and Karl Ekwall