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.

Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results

Felsani A;Moles A;Farsetti A;
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.
2014
Istituto di Biologia Cellulare e Neurobiologia - IBCN - Sede Monterotondo Scalo
Istituto di Biochimica e Biologia Cellulare - IBBC
ChIP-Seq
bioinformatics analysis
chromatin immunoprecipitation
next-generation sequencing
two-dimensional strandness-dependent electrophoresis
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.14243/246059
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