Titlebook: Chromatin Immunoprecipitation Assays; Methods and Protocol Philippe Collas Book 2009 Humana Press 2009 ChIP.DNA.DNA microarray.Genome-wide

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Epitope Tagging of Endogenous Proteins for Genome-Wide Chromatin Immunoprecipitation Analysis, .-DNA regulatory elements to which transcription factors bind. Nonetheless, the ChIP-chip technology requires antibodies with extremely high affinity and specificity for the target transcription factors. Unfortunately, such antibodies are not available for most human transcription factors. In princ

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Modeling and Analysis of ChIP-Chip Experiments,wever, the high density (several million genomic sequences for small eukaryote genomes) and the high noise-to-signal ratio of microarrays make the analysis of ChIP-chip data very challenging. In this chapter, we review some of the issues involved in the analysis of ChIP-chip data and present a few s

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DamID: A Methylation-Based Chromatin Profiling Approach,, R., 2007, .., 3027–3043; Kosak, S. T. and Groudine, M., 2004, .., 1371–1384). Our ability to understand the intimate interactions between proteins and the rapidly changing chromatin environment requires methods that will be able to provide accurate, sensitive, and unbiased mapping of these interac

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Chromosome Conformation Capture (from 3C to 5C) and Its ChIP-Based Modification,in is fixed with formaldehyde in vivo to cross-link interacting sites, digested with a restriction enzyme and ligated at a low DNA concentration so that ligation between cross-linked fragments is favored over ligation between random fragments. Ligation products are then analyzed and quantified by PC

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Determining Spatial Chromatin Organization of Large Genomic Regions Using 5C Technology,sses like metaphase and chromosome segregation. On a detailed level, long-range interactions between regulatory elements and promoters are essential for proper gene regulation. Microscopic techniques like FISH can detect chromatin contacts, although the resolution is generally low making detection o

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Analysis of Nascent RNA Transcripts by Chromatin RNA Immunoprecipitation, information on co-transcriptional regulation of nascent RNA came from invaluable in situ studies using single-cell model systems. More recently, the chromatin RNA immunoprecipitation technique has been developed to evaluate at the molecular level the association of proteins with nascent RNA which i