title: Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results.
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.
authors.forename: Armando
authors.initials: A
authors.lastname: Felsani
authors.forename: Bjarki
authors.initials: B
authors.lastname: Gudmundsson
authors.forename: Simona
authors.initials: S
authors.lastname: Nanni
authors.forename: Elena
authors.initials: E
authors.lastname: Brini
authors.forename: Anna
authors.initials: A
authors.lastname: Moles
authors.forename: Hans Guttormur
authors.initials: HG
authors.lastname: Thormar
authors.forename: Peter
authors.initials: P
authors.lastname: Estibeiro
authors.forename: Carlo
authors.initials: C
authors.lastname: Gaetano
authors.forename: Maurizio
authors.initials: M
authors.lastname: Capogrossi
authors.forename: Antonella
authors.initials: A
authors.lastname: Farsetti
authors.forename: Jon Johannes
authors.initials: JJ
authors.lastname: Jonsson
authors.forename: Alessandro
authors.initials: A
authors.lastname: Guffanti
mesh_terms: D000465:Algorithms; D000818:Animals; D001933:Brain Stem / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics*; D015180:Electrophoresis, Gel, Two-Dimensional; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods*; D013223:Statistics as Topic / Q000592:standards*
chemical_list: D004247:DNA
keywords: ChIP-Seq; bioinformatics analysis; chromatin immunoprecipitation; next-generation sequencing; two-dimensional strandness-dependent electrophoresis