title: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
abstract: Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305, USA.
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Landt
authors.forename: Georgi K
authors.initials: GK
authors.lastname: Marinov
authors.forename: Anshul
authors.initials: A
authors.lastname: Kundaje
authors.forename: Pouya
authors.initials: P
authors.lastname: Kheradpour
authors.forename: Florencia
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authors.lastname: Pauli
authors.forename: Serafim
authors.initials: S
authors.lastname: Batzoglou
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.forename: Peter
authors.initials: P
authors.lastname: Bickel
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.forename: Philip
authors.initials: P
authors.lastname: Cayting
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Chen
authors.forename: Gilberto
authors.initials: G
authors.lastname: DeSalvo
authors.forename: Charles
authors.initials: C
authors.lastname: Epstein
authors.forename: Katherine I
authors.initials: KI
authors.lastname: Fisher-Aylor
authors.forename: Ghia
authors.initials: G
authors.lastname: Euskirchen
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Jason
authors.initials: J
authors.lastname: Gertz
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Hartemink
authors.forename: Michael M
authors.initials: MM
authors.lastname: Hoffman
authors.forename: Vishwanath R
authors.initials: VR
authors.lastname: Iyer
authors.forename: Youngsook L
authors.initials: YL
authors.lastname: Jung
authors.forename: Subhradip
authors.initials: S
authors.lastname: Karmakar
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.forename: Qunhua
authors.initials: Q
authors.lastname: Li
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
authors.forename: Lijia
authors.initials: L
authors.lastname: Ma
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Milosavljevic
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Pazin
authors.forename: Marc D
authors.initials: MD
authors.lastname: Perry
authors.forename: Debasish
authors.initials: D
authors.lastname: Raha
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Reddy
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Noam
authors.initials: N
authors.lastname: Shoresh
authors.forename: Arend
authors.initials: A
authors.lastname: Sidow
authors.forename: Matthew
authors.initials: M
authors.lastname: Slattery
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.forename: Simon
authors.initials: S
authors.lastname: Xi
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Wold
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods; D017408:Guidelines as Topic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006657:Histones / Q000378:metabolism; D006801:Humans; D020407:Internet; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors