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

Genomnia S.r.l.
University of Iceland
Institute of Neuroscience
Lifeind ehf
I2Eye Diagnostics Ltd
Goethe University Frankfurt
IRCCS Istituto Dermopatico dell'Immacolata - Roma

Research output: Contribution to journal › Article

3 Citations (Scopus)

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.

Original language	English
Pages (from-to)	N/A-N/A
Journal	Briefings in Functional Genomics
DOIs	https://doi.org/10.1093/bfgp/elu001
Publication status	Published - 2014

Keywords

ChIP-Seq
bioinformatics analysis
chromatin immunoprecipitation
next-generation sequencing
two-dimensional strandness-dependent electrophoresis

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10.1093/bfgp/elu001

Cite this

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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.",

keywords = "ChIP-Seq, bioinformatics analysis, chromatin immunoprecipitation, next-generation sequencing, two-dimensional strandness-dependent electrophoresis, ChIP-Seq, bioinformatics analysis, chromatin immunoprecipitation, next-generation sequencing, two-dimensional strandness-dependent electrophoresis",

author = "Armando Felsani and Bjarki Gudmundsson and Simona Nanni and Elena Brini and Anna Moles and Thormar, \{Hans Guttormur\} and Peter Estibeiro and Carlo Gaetano and Maurizio Capogrossi and Antonella Farsetti and Jonsson, \{Jon Johannes\} and Alessandro Guffanti",

year = "2014",

doi = "10.1093/bfgp/elu001",

language = "English",

pages = "N/A--N/A",

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TY - JOUR

T1 - Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results

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 - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - ChIP-Seq

KW - bioinformatics analysis

KW - chromatin immunoprecipitation

KW - next-generation sequencing

KW - two-dimensional strandness-dependent electrophoresis

KW - ChIP-Seq

KW - bioinformatics analysis

KW - chromatin immunoprecipitation

KW - next-generation sequencing

KW - two-dimensional strandness-dependent electrophoresis

UR - http://hdl.handle.net/10807/60150

U2 - 10.1093/bfgp/elu001

DO - 10.1093/bfgp/elu001

M3 - Article

SN - 2041-2649

SP - N/A-N/A

JO - Briefings in Functional Genomics

JF - Briefings in Functional Genomics

ER -

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

Abstract

Keywords

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