title: ChIP-seq for genome-scale analysis of bacterial DNA-binding proteins.
abstract: Protein-DNA interactions are central to many basic biological processes, including transcription regulation, DNA replication, and DNA repair. Chromatin Immunoprecipitation (ChIP) is used to determine the position and strength of protein-DNA interactions in vivo. Coupling ChIP with microarrays (ChIP-chip), and more recently with deep sequencing (ChIP-seq), has allowed genome-wide profiling of DNA binding events in vivo. In this chapter we outline the steps to generate ChIP-seq libraries from bacterial samples and briefly discuss basic analysis of the data.
authors: Division of Genetics, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA, richard.bonocora@health.ny.gov.
authors: Richard P
authors: RP
authors: Bonocora
authors: Joseph T
authors: JT
authors: Wade
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004269:DNA, Bacterial / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics*; D015723:Gene Library; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008967:Molecular Biology / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins