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

Stephen G. Landt, Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, Peter Bickel, James B. Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles Epstein, Katherine I. Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J. Hartemink, Michael M. Hoffman, Vishwanath R. IyerYoungsook L. Jung, Subhradip Karmakar, Manolis Kellis, Peter V. Kharchenko, Qunhua Li, Tao Liu, X. Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, Richard M. Myers, Peter J. Park, Michael J. Pazin, Marc D. Perry, Debasish Raha, Timothy E. Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, John A. Stamatoyannopoulos, Michael Y. Tolstorukov, Kevin P. White, Simon Xi, Peggy J. Farnham, Jason D. Lieb, Barbara J. Wold, Michael Snyder

Research output: Contribution to journalArticle

727 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1813-1831
Number of pages19
JournalGenome Research
Volume22
Issue number9
DOIs
StatePublished - Sep 2012
Externally publishedYes

Fingerprint

Chromatin Immunoprecipitation
Practice Guidelines
Histone Code
Guidelines
High-Throughput Nucleotide Sequencing
Research Design
Transcription Factors
Antibodies

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

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 Research, 22(9), 1813-1831. https://doi.org/10.1101/gr.136184.111

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. / Landt, Stephen G.; Marinov, Georgi K.; Kundaje, Anshul; Kheradpour, Pouya; Pauli, Florencia; Batzoglou, Serafim; Bernstein, Bradley E.; Bickel, Peter; Brown, James B.; Cayting, Philip; Chen, Yiwen; DeSalvo, Gilberto; Epstein, Charles; Fisher-Aylor, Katherine I.; Euskirchen, Ghia; Gerstein, Mark; Gertz, Jason; Hartemink, Alexander J.; Hoffman, Michael M.; Iyer, Vishwanath R.; Jung, Youngsook L.; Karmakar, Subhradip; Kellis, Manolis; Kharchenko, Peter V.; Li, Qunhua; Liu, Tao; Liu, X. Shirley; Ma, Lijia; Milosavljevic, Aleksandar; Myers, Richard M.; Park, Peter J.; Pazin, Michael J.; Perry, Marc D.; Raha, Debasish; Reddy, Timothy E.; Rozowsky, Joel; Shoresh, Noam; Sidow, Arend; Slattery, Matthew; Stamatoyannopoulos, John A.; Tolstorukov, Michael Y.; White, Kevin P.; Xi, Simon; Farnham, Peggy J.; Lieb, Jason D.; Wold, Barbara J.; Snyder, Michael.

In: Genome Research, Vol. 22, No. 9, 09.2012, p. 1813-1831.

Research output: Contribution to journalArticle

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 2012, 'ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia', Genome Research, vol. 22, no. 9, pp. 1813-1831. 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 Research. 2012 Sep;22(9):1813-1831. https://doi.org/10.1101/gr.136184.111
Landt, Stephen G. ; Marinov, Georgi K. ; Kundaje, Anshul ; Kheradpour, Pouya ; Pauli, Florencia ; Batzoglou, Serafim ; Bernstein, Bradley E. ; Bickel, Peter ; Brown, James B. ; Cayting, Philip ; Chen, Yiwen ; DeSalvo, Gilberto ; Epstein, Charles ; Fisher-Aylor, Katherine I. ; Euskirchen, Ghia ; Gerstein, Mark ; Gertz, Jason ; Hartemink, Alexander J. ; Hoffman, Michael M. ; Iyer, Vishwanath R. ; Jung, Youngsook L. ; Karmakar, Subhradip ; Kellis, Manolis ; Kharchenko, Peter V. ; Li, Qunhua ; Liu, Tao ; Liu, X. Shirley ; Ma, Lijia ; Milosavljevic, Aleksandar ; Myers, Richard M. ; Park, Peter J. ; Pazin, Michael J. ; Perry, Marc D. ; Raha, Debasish ; Reddy, Timothy E. ; Rozowsky, Joel ; Shoresh, Noam ; Sidow, Arend ; Slattery, Matthew ; Stamatoyannopoulos, John A. ; Tolstorukov, Michael Y. ; White, Kevin P. ; Xi, Simon ; Farnham, Peggy J. ; Lieb, Jason D. ; Wold, Barbara J. ; Snyder, Michael. / ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. In: Genome Research. 2012 ; Vol. 22, No. 9. pp. 1813-1831.
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