title: Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.
abstract: DNA enrichment followed by sequencing (DNA-IP seq) is a versatile tool in molecular biology with a wide variety of applications. Computational analysis of differential DNA enrichment between conditions is important for identifying epigenetic alterations in disease compared to healthy controls and for revealing dynamic epigenetic modifications throughout normal and distorted cell differentiation and development. We present a protocol for genome-wide comparative analysis of DNA-IP sequencing data to identify statistically significant differential sequencing coverage between two conditions by considering variation across replicates. The protocol provides a detailed description for the comparative analysis of DNA-IP sequencing data including basic data processing, quality controls, and identification of differential enrichment using the Bioconductor package "MEDIPS".
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestr. 63 - 73, 14195, Berlin, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Lienhard
authors.affiliation: German Cancer Research Center, In Neuenheimer Feld 580, 69120, Heidelberg, Germany. l.chavez@dkfz.de.
authors.forename: Lukas
authors.initials: L
authors.lastname: Chavez
mesh_terms: D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D023281:Genomics / Q000379:methods* / Q000592:standards; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
keywords: Bioconductor; ChIP-seq; Computational biology; DNA enrichment; DNA methylation; Epigenetics; MeDIP-seq; Quality control; Sequencing