title: Semiconductor-based DNA sequencing of histone modification states.
abstract: The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Christine S
authors.initials: CS
authors.lastname: Cheng
authors.forename: Kunal
authors.initials: K
authors.lastname: Rai
authors.forename: Manuel
authors.initials: M
authors.lastname: Garber
authors.forename: Andrew
authors.initials: A
authors.lastname: Hollinger
authors.forename: Dana
authors.initials: D
authors.lastname: Robbins
authors.forename: Scott
authors.initials: S
authors.lastname: Anderson
authors.forename: Alyssa
authors.initials: A
authors.lastname: Macbeth
authors.forename: Austin
authors.initials: A
authors.lastname: Tzou
authors.forename: Mauricio O
authors.initials: MO
authors.lastname: Carneiro
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Gershenwald
authors.forename: Niall
authors.initials: N
authors.lastname: Lennon
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Lynda
authors.initials: L
authors.lastname: Chin
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D003713:Dendritic Cells / Q000166:cytology / Q000378:metabolism; D044127:Epigenesis, Genetic; D005260:Female; D015894:Genome, Human; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008545:Melanoma / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D011499:Protein Processing, Post-Translational; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods; D012878:Skin Neoplasms / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones