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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 microarray applications for the detection and characterization of genomic DNA-associated copy number alteration, loss of heterozygosity (LOH), cytosine methylation, protein binding 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(TM) series format, chapters include a brief introduction to their respective subjects, lists of the necessary materials and reagents, 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 biologist interested in understanding the principles of these analyses or in planning future experiments using microarrays to characterize the physical genome.
List of contents
Comparative Genomic Hybridization on BAC Arrays.- Comparative Genomic Hybridization on Spotted Oligonucleotide Microarrays.- Comparative Genomic Hybridization by Representational Oligonucleotide Microarray Analysis.- Application of Oligonucleotides Arrays for Coincident Comparative Genomic Hybridization, Ploidy Status and Loss of Heterozygosity Studies in Human Cancers.- Molecular Inversion Probe Assay for Allelic Quantitation.- A Whole-Genome Amplification Protocol for a Wide Variety of DNAs, Including Those from Formalin-Fixed and Paraffin-Embedded Tissue.- Algorithms for Calling Gains and Losses in Array CGH Data.- Methylation Analysis by Microarray.- Methylation Analysis by DNA Immunoprecipitation (MeDIP).- Combining Chromatin Immunoprecipitation and Oligonucleotide Tiling Arrays (ChIP-Chip) for Functional Genomic Studies.- ChIP-Chip: Algorithms for Calling Binding Sites.- Mapping Regulatory Elements by DNaseI Hypersensitivity Chip (DNase-Chip).- Microarray Analysis of DNA Replication Timing.- Integration of Diverse Microarray Data Types.
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 microarray applications for the detection and characterization of genomic DNA-associated copy number alteration, loss of heterozygosity (LOH), cytosine methylation, protein binding 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 reagents, 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 biologist interested in understanding the principles of these analyses or in planning future experiments using microarrays to characterize the physical genome.
