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What are the advantages of a ChIP Sequencing assay versus a ChIP-on-ChIP assay?

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What are the advantages of a ChIP Sequencing assay versus a ChIP-on-ChIP assay?

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Both types of assays, when carried out by Genpathway, are high-quality whole-genome assays. Advantages of ChIP Sequencing include a moderate increase in genome coverage due to repeat-masking of the arrays, increased resolution of the binding sites, the ability to carry out assays in any genome for which at least some genomic sequence and annotation is known vs. only human and mouse tiling arrays sets for ChIP-on-Chip, and a lower cost. One advantage for ChIP-on-Chip includes the option to carry out a scaled down version using promoter arrays. Also, some antibodies may enrich for sites present in highly repetitive regions such as centromeres, e.g., methylated DNA regions. ChIP Sequencing of this ChIP DNA may result in many tags that do not map uniquely and that dilute out sequencing of more informative regions. For these types of assays, ChIP-on-Chip may be better because repetitive regions are not represented on the arrays.

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