ChIP-seq data and analysis
The aim of a ChIP-seq experiment is to detect genomic regions where a protein is able to interact. This is achieved with the high-throughput sequencing of libraries obtained after chromatin-immunoprecipitation of the protein of interest.
ChIP-seq
The classical approach is to use an antibody to isolate protein-DNA complexes, and the independent characterization of each binding event with high-throughput sequencing techniques.
Johnson et al. Science (2007) and Robertson et al. Nature Methods(2007) were the first papers describing ChIP-seq experiments using short reads.
Kaufmann et al. PLoS Biology (2009) First ChIP-seq experiment in plants.
Kaufmann et al Nature Protocols (2010) Experimental and statistical description for plant ChIP-seq experiement
ChIA-PET
The same protein or protein complex can interact with several genomic regions at the same time, likely forming DNA loops. ChIA-PET aims to gather information regarding the interacting genomic regions involved on this loop formation
