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Bisulfite Conversion Efficiency


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#1 Boba

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Posted 28 April 2010 - 08:09 PM

Does anyone know what is the best way to determine bisulfite conversion efficiency? i.e. would MSP or bisulfite sequencing be used for this?
Also I am trying to optimize bisulfite conversion efficiency of FFPE samples....does anyone have experience with this?

#2 methylnick

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Posted 18 May 2010 - 06:00 PM

this is difficult to determine properly because the primers you use are designed to bias towards fully converted template.

Efficiency is then measured by cloning and sequencning methods where non-CpG C's sequenced are counted across all the clones sequenced.

Note this is only conversion efficiency of the region you are interested in and PCR amplified, and not necessarily a measure of efficiency across the whole genome. There are some sequence contexts where conversion could be inhibited by GC-content and secondary structures.




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