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Old 08-16-2012, 07:09 AM   #1
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Location: Leuven, Belgium

Join Date: Jun 2012
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Default BSSeq on whole genome - BS befor library prep?

Hi everyone,

My first post, so inform me if I'm not following the rules!

I am planning to perform BSSeq on genome scale on microbial DNA. Because I am a microbiologist and I am working with a genomics core nearby, I do not perform the library prep myself (they provide it for me). However in every BSSeq article the BS-treatment is done after the library prep (adition of adaptors). Also, because of the small genome size, we would want to multiplex by 96 samples on 1 lane of the Illumina HiSeq2000 with the Nextera Kit. To my understandings this kit is however not compatible with BSSeq because of nonmethylated adapters.

Is it possible to do BS-treament right after gDNA isolation (just with the EpitectKit of Qiagen for example), to do whole genome amplification of the DNA (to get higher amount + to get dsDNA and clean up the sample so that it meats the requirements of the core) with degenerated primers? (like they did in this one publication I found where they only did targeted sequencing: Mill et al, 2006 - Whole genome amplification of sodium bisulfite-treated DNA allows the accurate estimate of methylated cytosine density in limited DNA resources, BioTechniques 41:603-607, doi10.2144/000112266, see attach)

thanx in advance,

Last edited by BramVDBe; 08-16-2012 at 07:10 AM. Reason: to fast posted
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bisulfite sequencing, epigenetics, library preparation, whole genome amplifcation, whole genome sequencing

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