ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
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DOI：
10.1101/gr.136184.111
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发表时间：
2012-09
期刊：
影响因子：
7
通讯作者：
Snyder M
中科院分区：
文献类型：
--
作者：
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
染色质免疫沉淀（ChIP）和高通量DNA测序（ChIP-seq）已经成为一种有价值且广泛使用的方法，用于绘制活细胞中转录因子结合和组蛋白修饰的基因组位置。尽管它被广泛使用，但在如何进行这些实验、如何对结果进行评分和质量评估以及如何将数据和元数据存档以供公众使用方面存在相当大的差异。这些做法影响到任何全球ChIP实验的质量和效用。通过我们在执行ChIP-seq实验的经验，ENCODE和modENCODE联盟已经制定了一套工作标准和指南，用于芯片实验，并定期更新。目前的指南涉及抗体验证、实验复制、测序深度、数据和元数据报告以及数据质量评估。我们将讨论以这些方式评估的ChIP质量如何影响ChIP-seq数据的不同用途。分析中使用的所有数据集都已存放在ENCODE （http://encodeproject.org/ENCODE/）和modENCODE （http://www.modencode.org/）门户网站上供公众查看和下载。
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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影响因子：
64.8
作者：
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.
通讯作者：
Bernstein, Bradley E.
影响因子：
30.8
作者：
He, Qiye;Bardet, Anais F.;Zeitlinger, Julia
通讯作者：
Zeitlinger, Julia
DOI：
10.1073/pnas.1016959108
发表时间：
2011-04-05
影响因子：
11.1
作者：
He, Aibin;Kong, Sek Won;Pu, William T.
通讯作者：
Pu, William T.
影响因子：
14.9
作者：
Contrino S;Smith RN;Butano D;Carr A;Hu F;Lyne R;Rutherford K;Kalderimis A;Sullivan J;Carbon S;Kephart ET;Lloyd P;Stinson EO;Washington NL;Perry MD;Ruzanov P;Zha Z;Lewis SE;Stein LD;Micklem G
通讯作者：
Micklem G
影响因子：
46.9
作者：
Ji, Hongkai;Jiang, Hui;Ma, Wenxiu;Johnson, David S.;Myers, Richard M.;Wong, Wing H.
通讯作者：
Wong, Wing H.