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J Genet Genomics. 2013 May 20;40(5):249-60. doi: 10.1016/j.jgg.2013.03.010. Epub 2013 Mar 30.

An integrated workflow for DNA methylation analysis.

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Department of Plant & Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.


The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (, along with small RNA, RNA-seq and other data types.

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