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 -