Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results.
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.
['Felsani|Armando|A|', 'Gudmundsson|Bjarki|B|', 'Nanni|Simona|S|', 'Brini|Elena|E|', 'Moles|Anna|A|', 'Thormar|Hans Guttormur|HG|', 'Estibeiro|Peter|P|', 'Gaetano|Carlo|C|', 'Capogrossi|Maurizio|M|', 'Farsetti|Antonella|A|', 'Jonsson|Jon Johannes|JJ|', 'Guffanti|Alessandro|A|']
D000465:Algorithms D000818:Animals D001933:Brain Stem D047369:Chromatin Immunoprecipitation D019295:Computational Biology D004247:DNA D015180:Electrophoresis, Gel, Two-Dimensional D051379:Mice D017422:Sequence Analysis, DNA D013223:Statistics as Topic
ChIP-Seq bioinformatics analysis chromatin immunoprecipitation next-generation sequencing two-dimensional strandness-dependent electrophoresis