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

Risultato della ricerca: Contributo in rivistaArticolo in rivista

3 Citazioni (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.
Lingua originaleEnglish
pagine (da-a)156-162
Numero di pagine7
RivistaBriefings in Functional Genomics
Volume14
DOI
Stato di pubblicazionePubblicato - 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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