Bisulfite Sequence Analyses Using CyVerse Discovery Environment: From Mapping to DMRs

Q1 Agricultural and Biological Sciences Current protocols in plant biology Pub Date : 2016-09-01 DOI:10.1002/cppb.20034

Jawon Song, Greg Zynda, Samuel Beck, Nathan M. Springer, Matthew W. Vaughn

引用次数: 4

Abstract

Epigenetic modification of DNA through methylation is known to be involved in multiple biological processes such as gene suppression. However, the exact mechanism of how DNA methylations play their part is yet unclear. In mammals, CpG islands (CGI) have been studied extensively for their involvement in cancer. Whereas in plants, despite the fact that there are not only CpG but also CHG and CHH contexts of methylation, an efficient and easy-to-use pipeline to decipher these phenomena is still to be developed. Both ZED-align and BisuKit are user-friendly apps deployed on CyVerse infrastructure where users can use their bisulfite sequence files to run multiple command line-based packages with minimal intervention. © 2016 by John Wiley & Sons, Inc.

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利用CyVerse发现环境分析亚硫酸氢盐序列:从绘图到DMRs

DNA的表观遗传修饰通过甲基化被认为涉及多种生物过程，如基因抑制。然而，DNA甲基化如何发挥作用的确切机制尚不清楚。在哺乳动物中，CpG岛(CGI)因其与癌症的关系而被广泛研究。然而，在植物中，尽管甲基化不仅存在CpG背景，也存在CHG和CHH背景，但一种有效且易于使用的管道仍有待开发。ZED-align和BisuKit都是部署在CyVerse基础设施上的用户友好型应用程序，用户可以使用他们的亚硫酸盐序列文件来运行多个基于命令行的软件包，而无需干预。©2016 by John Wiley &儿子,Inc。

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Current protocols in plant biology Agricultural and Biological Sciences-Plant Science

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期刊介绍： Sound and reproducible laboratory methods are the foundation of scientific discovery. Yet nuances that are critical for an experiment''s success are not captured in the primary literature but exist only as part of a lab''s oral tradition. Current Protocols in Plant Biology provides reproducible step-by-step instructions for protocols relevant to plant research. Furthermore, Current Protocols content is thoughtfully organized by topic for optimal usage and to maximize contextual knowledge. Quarterly issues allow Current Protocols in Plant Biology to constantly evolve to keep pace with the newest discoveries and developments. Current Protocols in Plant Biology is the comprehensive source for protocols in the multidisciplinary field of plant biology, providing an extensive range of protocols from basic to cutting edge. Coverage includes: Extraction and analysis of DNA, RNA, proteins Chromosome analysis Transcriptional analysis Protein expression Metabolites Plant enzymology Epigenetics Plant genetic transformation Mutagenesis Arabidopsis, Maize, Poplar, Rice, and Soybean, and more.