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

被引：1321

作者：

Landt, Stephen G. ^{[4
]}

Marinov, Georgi K. ^{[5
]}

Kundaje, Anshul ^{[6
]}

Kheradpour, Pouya ^{[7
]}

Pauli, Florencia ^{[8
]}

Batzoglou, Serafim ^{[6
]}

Bernstein, Bradley E. ^{[9
]}

Bickel, Peter ^{[10
]}

Brown, James B. ^{[10
]}

Cayting, Philip ^{[4
]}

Chen, Yiwen ^{[11
]}

DeSalvo, Gilberto ^{[5
]}

Epstein, Charles ^{[9
]}

Fisher-Aylor, Katherine I. ^{[5
]}

Euskirchen, Ghia ^{[4
]}

Gerstein, Mark ^{[12
]}

Gertz, Jason ^{[8
]}

Hartemink, Alexander J. ^{[13
,14
]}

Hoffman, Michael M. ^{[15
]}

Iyer, Vishwanath R. ^{[16
]}

Jung, Youngsook L. ^{[17
,18
]}

Karmakar, Subhradip ^{[19
]}

Kellis, Manolis ^{[7
]}

Kharchenko, Peter V. ^{[16
]}

Li, Qunhua ^{[20
]}

Liu, Tao ^{[11
]}

Liu, X. Shirley ^{[11
]}

Ma, Lijia ^{[19
]}

Milosavljevic, Aleksandar ^{[21
]}

Myers, Richard M. ^{[8
]}

Park, Peter J. ^{[17
,18
]}

Pazin, Michael J. ^{[22
]}

Perry, Marc D. ^{[23
]}

Raha, Debasish ^{[24
]}

Reddy, Timothy E. ^{[8
]}

Rozowsky, Joel ^{[12
]}

Shoresh, Noam ^{[9
]}

Sidow, Arend ^{[4
,25
]}

Slattery, Matthew ^{[19
]}

Stamatoyannopoulos, John A. ^{[15
,26
]}

Tolstorukov, Michael Y. ^{[17
,18
]}

White, Kevin P. ^{[19
]}

Xi, Simon ^{[27
]}

Farnham, Peggy J. ^{[1
]}

Lieb, Jason D. ^{[2
,3
]}

Wold, Barbara J. ^{[5
]}

Snyder, Michael ^{[4
]}

机构：

[1] Univ So Calif, Dept Biochem & Mol Biol, Kenneth Norris Jr Comprehens Canc Ctr, Los Angeles, CA 90089 USA

[2] Univ N Carolina, Dept Biol, Carolina Ctr Genome Sci, Chapel Hill, NC 27599 USA

[3] Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA

[4] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[5] CALTECH, Div Biol, Pasadena, CA 92116 USA

[6] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[7] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

[8] HudsonAlpha Inst Biotechnol, Huntsville, AL 35806 USA

[9] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[10] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[11] Harvard Univ, Sch Publ Hlth, Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[12] Yale Univ, Computat Biol & Bioinformat Program, New Haven, CT 06511 USA

[13] Duke Univ, Dept Comp Sci, Durham, NC 27708 USA

[14] Duke Univ, Ctr Syst Biol, Durham, NC 27708 USA

[15] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[16] Univ Texas Austin, Inst Cellular & Mol Biol, Sect Mol Genet & Microbiol, Ctr Syst & Synthet Biol, Austin, TX 78701 USA

[17] Harvard Univ, Ctr Biomed Informat, Sch Med, Boston, MA 02115 USA

[18] Brigham & Womens Hosp, Div Genet, Dept Med, Boston, MA 02115 USA

[19] Univ Chicago, Inst Genom & Syst Biol, Chicago, IL 60637 USA

[20] Penn State Univ, Dept Stat, University Pk, PA 16802 USA

[21] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[22] NHGRI, NIH, Rockville, MD 20852 USA

[23] Ontario Inst Canc Res, Toronto, ON MSG 0A3, Canada

[24] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06511 USA

[25] Stanford Univ, Dept Pathol, Stanford, CA 94305 USA

[26] Univ Washington, Dept Med, Seattle, WA 98195 USA

[27] Univ Massachusetts, Sch Med, Worcester, MA 01655 USA

来源：

GENOME RESEARCH | 2012年 / 22卷 / 09期

基金：

美国国家科学基金会;

关键词：

TRANSCRIPTION FACTOR-BINDING; GENOME-WIDE ANALYSIS; CHROMATIN IMMUNOPRECIPITATION; IDENTIFICATION; METHYLATIONS; ASSOCIATION; MACROPHAGE; EXPRESSION; ELEMENTS; REGIONS;

D O I：

10.1101/gr.136184.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1813 / 1831

页数：19

共 50 条

[1] Mapping accessible chromatin regions using Sono-Seq [J].

Auerbach, Raymond K. ;

Euskirchen, Ghia ;

Rozowsky, Joel ;

Lamarre-Vincent, Nathan ;

Moqtaderi, Zarmik ;

Lefrancois, Philippe ;

Struhl, Kevin ;

Gerstein, Mark ;

Snyder, Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (35) :14926-14931

[2] High-resolution profiling of histone methylations in the human genome [J].

Barski, Artern ;

Cuddapah, Suresh ;

Cui, Kairong ;

Roh, Tae-Young ;

Schones, Dustin E. ;

Wang, Zhibin ;

Wei, Gang ;

Chepelev, Iouri ;

Zhao, Keji .

CELL, 2007, 129 (04) :823-837

[3] Unlocking the secrets of the genome [J].

Celniker, Susan E. ;

Dillon, Laura A. L. ;

Gerstein, Mark B. ;

Gunsalus, Kristin C. ;

Henikoff, Steven ;

Karpen, Gary H. ;

Kellis, Manolis ;

Lai, Eric C. ;

Lieb, Jason D. ;

MacAlpine, David M. ;

Micklem, Gos ;

Piano, Fabio ;

Snyder, Michael ;

Stein, Lincoln ;

White, Kevin P. ;

Waterston, Robert H. .

NATURE, 2009, 459 (7249) :927-930

[4] modMine: flexible access to modENCODE data [J].

Contrino, Sergio ;

Smith, Richard N. ;

Butano, Daniela ;

Carr, Adrian ;

Hu, Fengyuan ;

Lyne, Rachel ;

Rutherford, Kim ;

Kalderimis, Alex ;

Sullivan, Julie ;

Carbon, Seth ;

Kephart, Ellen T. ;

Lloyd, Paul ;

Stinson, E. O. ;

Washington, Nicole L. ;

Perry, Marc D. ;

Ruzanov, Peter ;

Zha, Zheng ;

Lewis, Suzanna E. ;

Stein, Lincoln D. ;

Micklem, Gos .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D1082-D1088

[5] Regulation of B lymphocyte and macrophage development by graded expression of PU.1 [J].

DeKoter, RP ;

Singh, H .

SCIENCE, 2000, 288 (5470) :1439-1441

[6] Substantial biases in ultra-short read data sets from high-throughput DNA sequencing [J].

Dohm, Juliane C. ;

Lottaz, Claudio ;

Borodina, Tatiana ;

Himmelbauer, Heinz .

NUCLEIC ACIDS RESEARCH, 2008, 36 (16)

[7] An assessment of histone-modification antibody quality [J].

Egelhofer, Thea A. ;

Minoda, Aki ;

Klugman, Sarit ;

Lee, Kyungjoon ;

Kolasinska-Zwierz, Paulina ;

Alekseyenko, Artyom A. ;

Cheung, Ming-Sin ;

Day, Daniel S. ;

Gadel, Sarah ;

Gorchakov, Andrey A. ;

Gu, Tingting ;

Kharchenko, Peter V. ;

Kuan, Samantha ;

Latorre, Isabel ;

Linder-Basso, Daniela ;

Luu, Ying ;

Ngo, Queminh ;

Perry, Marc ;

Rechtsteiner, Andreas ;

Riddle, Nicole C. ;

Schwartz, Yuri B. ;

Shanower, Gregory A. ;

Vielle, Anne ;

Ahringer, Julie ;

Elgin, Sarah C. R. ;

Kuroda, Mitzi I. ;

Pirrotta, Vincenzo ;

Ren, Bing ;

Strome, Susan ;

Park, Peter J. ;

Karpen, Gary H. ;

Hawkins, R. David ;

Lieb, Jason D. .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2011, 18 (01) :91-+

[8] Mapping and analysis of chromatin state dynamics in nine human cell types [J].

Ernst, Jason ;

Kheradpour, Pouya ;

Mikkelsen, Tarjei S. ;

Shoresh, Noam ;

Ward, Lucas D. ;

Epstein, Charles B. ;

Zhang, Xiaolan ;

Wang, Li ;

Issner, Robbyn ;

Coyne, Michael ;

Ku, Manching ;

Durham, Timothy ;

Kellis, Manolis ;

Bernstein, Bradley E. .

NATURE, 2011, 473 (7345) :43-U52

[9] Discovery and characterization of chromatin states for systematic annotation of the human genome [J].

Ernst, Jason ;

Kellis, Manolis .

NATURE BIOTECHNOLOGY, 2010, 28 (08) :817-U94

[10] The ENCODE (ENCyclopedia of DNA elements) Project [J].

Feingold, EA ;

Good, PJ ;

Guyer, MS ;

Kamholz, S ;

Liefer, L ;

Wetterstrand, K ;

Collins, FS ;

Gingeras, TR ;

Kampa, D ;

Sekinger, EA ;

Cheng, J ;

Hirsch, H ;

Ghosh, S ;

Zhu, Z ;

Pate, S ;

Piccolboni, A ;

Yang, A ;

Tammana, H ;

Bekiranov, S ;

Kapranov, P ;

Harrison, R ;

Church, G ;

Struhl, K ;

Ren, B ;

Kim, TH ;

Barrera, LO ;

Qu, C ;

Van Calcar, S ;

Luna, R ;

Glass, CK ;

Rosenfeld, MG ;

Guigo, R ;

Antonarakis, SE ;

Birney, E ;

Brent, M ;

Pachter, L ;

Reymond, A ;

Dermitzakis, ET ;

Dewey, C ;

Keefe, D ;

Denoeud, F ;

Lagarde, J ;

Ashurst, J ;

Hubbard, T ;

Wesselink, JJ ;

Castelo, R ;

Eyras, E ;

Myers, RM ;

Sidow, A ;

Batzoglou, S .

SCIENCE, 2004, 306 (5696) :636-640

← 1 2 3 4 5 →