title: Automating ChIP-seq experiments to generate epigenetic profiles on 10,000 HeLa cells.
abstract: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of the major limitations is the requirement for high amounts of starting material, usually millions of cells. Automation of chromatin immunoprecipitation assays is possible when the procedure is based on the use of magnetic beads. Successful automated protocols of chromatin immunoprecipitation and library preparation have been specifically designed on a commercially available robotic liquid handling system dedicated mainly to automate epigenetic assays. First, validation of automated ChIP-seq assays using antibodies directed against various histone modifications was shown, followed by optimization of the automated protocols to perform chromatin immunoprecipitation and library preparation starting with low cell numbers. The goal of these experiments is to provide a valuable tool for future epigenetic analysis of specific cell types, sub-populations, and biopsy samples.
authors.affiliation: Diagenode S.A.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Berguet
authors.affiliation: Diagenode S.A.
authors.forename: Jan
authors.initials: J
authors.lastname: Hendrickx
authors.affiliation: Diagenode S.A.
authors.forename: Celine
authors.initials: C
authors.lastname: Sabatel
authors.affiliation: Diagenode S.A.
authors.forename: Miklos
authors.initials: M
authors.lastname: Laczik
authors.affiliation: Diagenode Inc.
authors.forename: Sharon
authors.initials: S
authors.lastname: Squazzo
authors.affiliation: Diagenode Inc.; ignacio.mazon@diagenode.com.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Mazon Pelaez
authors.affiliation: Diagenode Inc.; rsa@diagenode.com.
authors.forename: Rini
authors.initials: R
authors.lastname: Saxena
authors.affiliation: Diagenode S.A.
authors.forename: Helene
authors.initials: H
authors.lastname: Pendeville
authors.affiliation: Diagenode S.A.
authors.forename: Dominique
authors.initials: D
authors.lastname: Poncelet
mesh_terms: D001331:Automation / Q000379:methods; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000235:genetics; D057890:Epigenomics / Q000379:methods; D015723:Gene Library; D006367:HeLa Cells / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025941:Protein Interaction Mapping; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004247:DNA