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

Contributor(s): Pollack, Jonathan R
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 556.; Springer protocols (Series): Publisher: New York : Humana, ©2009Description: 1 online resource (x, 223 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781603271912; 1603271910; 9781603271929; 1603271929Subject(s): DNA microarrays -- Laboratory manuals | Genomics -- Laboratory manuals | Genome | Microarray Analysis -- methods | DNA -- analysis | Genetic Phenomena | DNA microarrays | GenomicsGenre/Form: Laboratory Manual. | Electronic books. | Laboratory manuals. Additional physical formats: Print version:: Microarray analysis of the physical genome.DDC classification: 611.01816 LOC classification: QP624.5.D726 | M5118 2009Online resources: Click here to access online
Contents:
DNA microarray technology. Introduction / J.R. Pollack -- Comparative genomic hybridization on BAC arrays / B.P. Coe [and others] -- Comparative genomic hybridization on spotted oligonucleotide microarrays / Y.H. Kim and J.R. Pollack -- Comparative genomic hybridization by representational oligonucleotide microarray analysis / R. Lucito and J. Byrnes -- Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers / J.K. Cowell and K.C. Lo -- Molecular inversion probe assay for allelic quantitation / H. Ji and K. Welch -- A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue / P.L. Paris -- Algorithms for calling gains and losses in array CGH data / P. Wang -- Methylation analysis by microarray / D.E. Deatherage [and others] -- Methylation analysis by DNA immunoprecipitation (MeDIP) / E.A. Vucic [and others] -- Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies / J. Eeckhoute, M. Lupien and M. Brown -- ChIP-Chip: algorithms for calling binding sites / X.S. Liu and C.A. Meyer -- Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip) / Y. Shibata and G.E. Crawford -- Microarray analysis of DNA replication timing / N. Karnani, C.M. Taylor and A. Dutta -- Integration of diverse microarray data types / K. Salari and J.R. Pollack.
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.
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Includes bibliographical references and index.

DNA microarray technology. Introduction / J.R. Pollack -- Comparative genomic hybridization on BAC arrays / B.P. Coe [and others] -- Comparative genomic hybridization on spotted oligonucleotide microarrays / Y.H. Kim and J.R. Pollack -- Comparative genomic hybridization by representational oligonucleotide microarray analysis / R. Lucito and J. Byrnes -- Application of oligonucleotides arrays for coincident comparative genomic hybridization, ploidy status and loss of heterozygosity studies in human cancers / J.K. Cowell and K.C. Lo -- Molecular inversion probe assay for allelic quantitation / H. Ji and K. Welch -- A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue / P.L. Paris -- Algorithms for calling gains and losses in array CGH data / P. Wang -- Methylation analysis by microarray / D.E. Deatherage [and others] -- Methylation analysis by DNA immunoprecipitation (MeDIP) / E.A. Vucic [and others] -- Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies / J. Eeckhoute, M. Lupien and M. Brown -- ChIP-Chip: algorithms for calling binding sites / X.S. Liu and C.A. Meyer -- Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip) / Y. Shibata and G.E. Crawford -- Microarray analysis of DNA replication timing / N. Karnani, C.M. Taylor and A. Dutta -- Integration of diverse microarray data types / K. Salari and J.R. Pollack.

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.

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