title: ChIP sequencing to identify p53 targets.
abstract: Mutant p53 may activate target genes through the interaction of transcription factors or through histone modifications. Chromatin immunoprecipitation (ChIP) is a method commonly used to study these types of protein interactions. In order to generate a list of target genes that may be activated through this mechanism, ChIP sequencing may be used. ChIP sequencing involves the mass parallel sequencing of ChIP DNA fragments. We describe a method by which to prepare chromatin immunoprecipitation sequencing libraries and how to analyze sequencing data. In this procedure, prepared libraries have been sent to a core facility. The results have been verified using quantitative PCR.
authors.affiliation: Department of Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Vaughan
authors.forename: Brad
authors.initials: B
authors.lastname: Windle
authors.forename: Sumitra
authors.initials: S
authors.lastname: Deb
mesh_terms: D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology; D004247:DNA / Q000235:genetics / Q000302:isolation & purification*; D053938:DNA Fragmentation; D015894:Genome, Human; D006801:Humans; D046210:Microfluidic Analytical Techniques / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
chemical_list: D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53; D004247:DNA