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.