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

Armando Felsani; Bjarki Gudmundsson; Simona Nanni; Elena Brini; Anna Moles; Hans Guttormur Thormar; Peter Estibeiro; Carlo Gaetano; Maurizio Capogrossi; Antonella Farsetti; Jon Johannes Jonsson; Alessandro Guffanti

doi:10.1093/bfgp/elu001

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

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

Research output: Contribution to journal › Article › peer-review

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 language	English (US)
Pages (from-to)	156-162
Number of pages	7
Journal	Briefings in Functional Genomics
Volume	14
Issue number	2
DOIs	https://doi.org/10.1093/bfgp/elu001
State	Published - Mar 1 2015
Externally published	Yes

Keywords

Bioinformatics analysis
ChIP-Seq
Chromatin immunoprecipitation
Next-generation sequencing
Two-dimensional strandness-dependent electrophoresis

ASJC Scopus subject areas

Biochemistry
Molecular Biology
Genetics

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10.1093/bfgp/elu001

Cite this

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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.",

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AU - Felsani, Armando

AU - Gudmundsson, Bjarki

AU - Nanni, Simona

AU - Brini, Elena

AU - Moles, Anna

AU - Thormar, Hans Guttormur

AU - Estibeiro, Peter

AU - Gaetano, Carlo

AU - Capogrossi, Maurizio

AU - Farsetti, Antonella

AU - Jonsson, Jon Johannes

AU - Guffanti, Alessandro

PY - 2015/3/1

Y1 - 2015/3/1

N2 - 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.

AB - 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.

KW - Bioinformatics analysis

KW - ChIP-Seq

KW - Chromatin immunoprecipitation

KW - Next-generation sequencing

KW - Two-dimensional strandness-dependent electrophoresis

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

Abstract

Keywords

ASJC Scopus subject areas

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