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

Simona Nanni, Armando Felsani, Bjarki Gudmundsson, Anna Moles, Hans Guttormur Thormar, Peter Estibeiro, Carlo Gaetano, Maurizio Capogrossi, Jon Johannes Jonsson, Alessandro Guffanti

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)156-162
Number of pages7
JournalBriefings in Functional Genomics
Volume14
DOIs
Publication statusPublished - 2015

Keywords

  • Algorithms
  • Animals
  • Biochemistry
  • Bioinformatics analysis
  • Brain Stem
  • ChIP-Seq
  • Chromatin Immunoprecipitation
  • Chromatin immunoprecipitation
  • Computational Biology
  • DNA
  • Electrophoresis, Gel, Two-Dimensional
  • Genetics
  • Mice
  • Molecular Biology
  • Next-generation sequencing
  • Sequence Analysis, DNA
  • Statistics as Topic
  • Two-dimensional strandness-dependent electrophoresis

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