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Felsani A.,Scientific consultant of Genomnia s.r.l. | Gudmundsson B.,University of Iceland | Nanni S.,Catholic University | Brini E.,Catholic University | And 8 more authors.
Briefings in Functional Genomics | Year: 2015

Different ChIP-Seq protocolsmay have a significant impact on the final outcome in terms of quality, number and distribution of called peaks. Sample DNA undergoes a long procedure before the final sequencing step, and damaged DNA can result in excessive mismatches in the alignment with reference genome. In this letter, we present the effect of well-defined modifications (timing of formaldehyde crosslink reversal, brand of the sonicator) of standard ChIP-Seq protocol on parallel samples derived from the same cell line correlating the initial DNA quality control metrics to the final bioinformatics analysis results. © The Author 2014. Published by Oxford University Press. All rights reserved.

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