Different ChIP-Seq protocols may 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.
Felsani, A., Gudmundsson, B., Nanni, S., Brini, E., Moles, A., Thormar, H., Estibeiro, P., Gaetano, C., Capogrossi, M., Farsetti, A., Jonsson, J., Guffanti, A., Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results, <<BRIEFINGS IN FUNCTIONAL GENOMICS>>, 2014; (N/A): N/A-N/A. [doi:10.1093/bfgp/elu001] [http://hdl.handle.net/10807/60150]
Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results
Nanni, Simona;
2014
Abstract
Different ChIP-Seq protocols may 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.
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