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DNA methylation is known as an important regulation of genome function. It has effects on the binding affinity between DNA and DNA binding proteins, resulting to varies of biological results. DNA methylation can be a dynamic process for altering gene activity temporarily, or be long-term changes upon cell differentiation/ cell fate commitment. It plays roles in epigenetic regulation on genome functions. Using bisulfite conversion of genomic DNA combining with next-generation sequencing (BS Seq), the 5-mehtylcytosine level of all available C residues in the whole genome scale can be detected.
To fasiliate the access of the BS Seq data for model plant Arabidopsis researchers,
we build the TEA workbench. Present compatible referenece genome/ annotation in TEA
is TAIR10. Please check gtf section for details. Mapping reports
from two popular bisulfite sequence mapping programs,
from BS Seeker 2, and
Bismark, are supported.
We adopt mtable, a summarized score to indicate the methylation level of three different 5-methylC sequence contexts (CG, CHG, CHH) for each gene. Please check the BS Seq mapping process to get a quick overview if you are not familiar with the mapping process.