title: Assay for Transposase-Accessible Chromatin Using Sequencing (ATAC-seq) Data Analysis.
abstract: The study of epigenetic properties of the human genome, including structural modifications of DNA and chromatin, has increased tremendously as mounting evidence has demonstrated how much epigenetics affects human gene expression. Buenrostro et al. have developed a rapid method, requiring low numbers of living cells as input, for examining chromatin accessibility across the epigenome, known as the assay for transposase-accessible chromatin using sequencing (ATAC-seq). The overall goal of this unit is to provide a thorough ATAC-seq data analysis plan, as well as describe how primary human blood samples can be processed for use in ATAC-seq. In addition, a number of quality control parameters are discussed to ensure the integrity and confidence in the ATAC-seq data. © 2017 by John Wiley & Sons, Inc.
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio.
authors.forename: Kristy L S
authors.initials: KLS
authors.lastname: Miskimen
authors.affiliation: Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio.
authors.forename: E Ricky
authors.initials: ER
authors.lastname: Chan
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio.|Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Haines
mesh_terms: D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D006801:Humans; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D019895:Transposases / Q000378:metabolism*
chemical_list: D002843:Chromatin; D004247:DNA; D019895:Transposases
keywords: ATAC-seq; chromatin accessibility; epigenetics; peak-calling