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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Publication ,  Journal Article
Landt, SG; Marinov, GK; Kundaje, A; Kheradpour, P; Pauli, F; Batzoglou, S; Bernstein, BE; Bickel, P; Brown, JB; Cayting, P; Chen, Y; Gertz, J ...
Published in: Genome Res
September 2012

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.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

September 2012

Volume

22

Issue

9

Start / End Page

1813 / 1831

Location

United States

Related Subject Headings

  • Transcription Factors
  • Internet
  • Humans
  • Histones
  • High-Throughput Nucleotide Sequencing
  • Guidelines as Topic
  • Genomics
  • Genome
  • Databases, Genetic
  • Chromatin Immunoprecipitation
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., … Snyder, M. (2012). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res, 22(9), 1813–1831. https://doi.org/10.1101/gr.136184.111
Landt, Stephen G., Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, et al. “ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.Genome Res 22, no. 9 (September 2012): 1813–31. https://doi.org/10.1101/gr.136184.111.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813–31.
Landt, Stephen G., et al. “ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.Genome Res, vol. 22, no. 9, Sept. 2012, pp. 1813–31. Pubmed, doi:10.1101/gr.136184.111.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813–1831.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

September 2012

Volume

22

Issue

9

Start / End Page

1813 / 1831

Location

United States

Related Subject Headings

  • Transcription Factors
  • Internet
  • Humans
  • Histones
  • High-Throughput Nucleotide Sequencing
  • Guidelines as Topic
  • Genomics
  • Genome
  • Databases, Genetic
  • Chromatin Immunoprecipitation