A quality control system for profiles obtained by ChIP sequencing

作者：Mendoza Parra Marco Antonio^*; Van Gool Wouter; Saleem Mohamed Ashick Mohamed; Ceschin Danilo Guillermo; Gronemeyer Hinrich

来源：Nucleic Acids Research, 2013, 41(21): e196.

DOI：10.1093/nar/gkt829

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 %26gt; 5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses.

• 出版日期2013-11