Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become an essential tool for epigenetic scientists. ChIP-seq is used to map protein-DNA interactions and epigenetic marks such as histone modifications at the genome-wide level. Here we describe a complete ChIP-seq laboratory protocol (tailored toward processing tissue samples as well as cell lines) and the bioinformatic pipelines utilized for handling raw sequencing files through to peak calling.
Keywords: Antibodies; Bioinformatic pipelines; Bioinformatics; ChIP-seq; ChIP-seq data processing; Chromatin immunoprecipitation and high-throughput sequencing; DNA library assembly; Genome alignment; Peak calling.