Microarray analysis of the physical genome : methods and protocols / edited by Jonathan R. Pollack.

Format:

Book

Contributor:

Pollack, Jonathan R.

Series:

Methods in molecular biology (Clifton, N.J.) 1064-3745 ; v. 556.

Methods in molecular biology ; 556

Language:

English

Subjects (All):

Genomics.

Genome--physiology.

Microarray Analysis--methods.

Gene Expression Profiling--methods.

Medical Subjects:

Genome--physiology.

Microarray Analysis--methods.

Gene Expression Profiling--methods.

Genre:

Laboratory manuals.

Physical Description:

x, 223 pages : illustrations ; 27 cm.

Place of Publication:

New York : Humana, 2009.

Summary:

In the early years of microarray technology, efforts were directed mainly at profiling expressed genes, while recently the microarray platform has been adapted into diverse applications directed toward the investigation of the physical genome. In Microarray Analysis of the Physical Genome: Methods and Protocols, experts in the field cover DNA microarrary applications for the detection and characterization of genomic DNA-associated copy number alternation, loss of heterozygosity (LOH), cytosine methylation, protein bindings sites, regulatory elements, and replication timing, with an emphasis on higher eukaryote (animal) and cancer genomes. Written in the highly successful Methods in Molecular Biology" series format, chapters include a brief introduction to their respective subjects, lists of the necessary materials and regents, step-by-step protocols, and time-saving notes on troubleshooting and avoiding known pitfalls.

Authoritative and easy-to-use, Microarray Analysis of the Physical Genome: Methods and Protocols is of great value to the molecular biologist or computational biologists interested in understanding the principles of these analysis or in planning future experiments using microarrays to characterize the physical genome.

Contents:

1 Introduction / Jonathan R. Pollack 1

2 Comparative Genomic Hybridization on BAC Arrays / Bradley P. Coe, William W. Lockwood, Raj Chari, Wan L. Lam 7

3 Comparative Genomic Hybridization on Spotted Oligonucleotide Microarrarys / Young H. Kim, Jonathan R. Pollack 21

4 Comparative Genomic Hybridization by Representational Oligonucleotide Microarray Analysis / Robert Lucito, James Byrnes 33

5 Application of Obligonucleotides Arrays for Coincident Comparative Genomic Hybridization, Polidy Status and Loss of Heterozygosity Studies in Human Cancers / John K. Cowell, Ken C. Lo 47

6 Molecular Inversion Probe Assay for Allelic Quantitation / Hanlee Ji, Katrina Welch 67

7 A Whole-Genome Amplification Protocol for a Wide Variety of DNAs, Including Those from Formalin-Fixed and Paraffin-Embedded Tissue / Pamela L. Paris 89

8 Algorithms for Calling Gains and Losses in Array CGH Data / Pei Wang 99

9 Methylation Analysis by Microarray / Daniel E. Deatherage, Dustin Potter, Pearlly S. Yan, Tim H.-M. Huang, Shili Lin 117

10 Methylation Analysis by DNA Immunoprecipation (MeDIP) / Emily A. Vucic, Ian M. Wilson, Jennifer M. Campbell, Wan L. Lam 141

11 Combining Chromatin Immunoprecipitation and Oligonucleotide Tiling Arrays (ChIP-Chip) for Functional Genomic Studies / Jérôme Eckhoute, Mathieu Lupien, Myles Brown 155

12 ChIP-Chip: Algorithms for Calling Binding Sites / X. Shirley Liu, Clifford A. Meyer 165

13 Mapping Regulatory Elements by DNasel Hypersensitivity Chip (DNase-Chip) / Yoichiro Shibata, Gregory E. Crawford 177

14 Microarray Analysis of DNA Replication Timing / Neerja Karnani, Christopher M. Taylor, Anindya Dutta 191

15 Integration of Diverse Microarray Data Types / Keyan Salari, Jonathan R. Pollack 205.

Notes:

"Springer protocols"--Cover.

Includes bibliographical references and index.

ISBN:

1603271910

9781603271912

OCLC:

322349710