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 - 2015
Y1 - 2015
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 - Algorithms
KW - Animals
KW - Biochemistry
KW - Bioinformatics analysis
KW - Brain Stem
KW - ChIP-Seq
KW - Chromatin Immunoprecipitation
KW - Chromatin immunoprecipitation
KW - Computational Biology
KW - DNA
KW - Electrophoresis, Gel, Two-Dimensional
KW - Genetics
KW - Mice
KW - Molecular Biology
KW - Next-generation sequencing
KW - Sequence Analysis, DNA
KW - Statistics as Topic
KW - Two-dimensional strandness-dependent electrophoresis
KW - Algorithms
KW - Animals
KW - Biochemistry
KW - Bioinformatics analysis
KW - Brain Stem
KW - ChIP-Seq
KW - Chromatin Immunoprecipitation
KW - Chromatin immunoprecipitation
KW - Computational Biology
KW - DNA
KW - Electrophoresis, Gel, Two-Dimensional
KW - Genetics
KW - Mice
KW - Molecular Biology
KW - Next-generation sequencing
KW - Sequence Analysis, DNA
KW - Statistics as Topic
KW - Two-dimensional strandness-dependent electrophoresis
UR - http://hdl.handle.net/10807/131710
UR - http://bfg.oxfordjournals.org/content/14/2/156.full.pdf
U2 - 10.1093/bfgp/elu001
DO - 10.1093/bfgp/elu001
M3 - Article
SN - 2041-2649
VL - 14
SP - 156
EP - 162
JO - Briefings in Functional Genomics
JF - Briefings in Functional Genomics
ER -