title: A quality control system for profiles obtained by ChIP sequencing.
abstract: The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin immunoprecipitation (ChIP-seq) but also related enrichment-based studies like methylated DNA immunoprecipitation/methylated DNA binding domain sequencing, global run on sequencing or RNA-seq. Importantly, QC assessment may significantly improve multidimensional comparisons that have great promise for extracting information from combinatorial analyses of the global profiles established for chromatin modifications, the bindings of epigenetic and chromatin-modifying enzymes/machineries, RNA polymerases and transcription factors and total, nascent or ribosome-bound RNAs. Here we present an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. This QC system was used to certify >5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses.
authors.affiliation: Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, France.
authors.forename: Marco-Antonio
authors.initials: MA
authors.lastname: Mendoza-Parra
authors.forename: Wouter
authors.initials: W
authors.lastname: Van Gool
authors.forename: Mohamed Ashick
authors.initials: MA
authors.lastname: Mohamed Saleem
authors.forename: Danilo Guillermo
authors.initials: DG
authors.lastname: Ceschin
authors.forename: Hinrich
authors.initials: H
authors.lastname: Gronemeyer
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000592:standards*; D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000592:standards*
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