ABSTRACT
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is amongst the most widely used methods in molecular biology. In order to confidently identify enriched regions in a ChIP-seq sample, the read distribution needs to be compared to a background distribution to control for potential biases. The optimal control for a ChIP-seq experiment is to sequence the input DNA purified from the sheared chromatin before the antibody incubation step. ChIP-seq is an experiment based on antibody immunoprecipitation performed on a population of cells to define protein binding sites in the genome using high-throughput sequencing (HTS). Since its first introduction in 2005, HTS has been a rapidly evolving field, resulting in a broad spectrum of available library preparation protocols and sequencing technologies. DNA adenine methyltransferase identification works as an alternative to chromatin immunoprecipitation. Since ChIP-seq is an antibody-based immunoprecipitation experiment, its efficiency strongly depends on the quality and specificity of the antibody.
