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bisulfte conversion with Ampure XP beads in the solution

WGBS; RRBS; selection

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#1 et2b

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Posted 13 May 2015 - 01:40 AM

Dear all,

 

I wonder if anybody ever tried to do bisulfite conversion with Ampure XP beads (SPRI) in the solution?

I know zymo research has a magbeads protocol. But according to zymo their beads have no size selection properties.

 

What I would like to do is a protocol similar that of Fisher et al. http://genomebiology...content/12/1/R1

keeping all steps on Ampure XP beads...  (have very very little DNA...)

So fragmentation or restriction of gDNA, end-repair, adapter ligation, size selection of >150bp, bisulfite conversion, cleanup, desulfanation,cleanup 

 

best



#2 methylnick

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Posted 14 May 2015 - 01:18 PM

Cool paper, thanks for that, without knowing the specifics, I would suspect the salt concentrations required in the bisulfite reaction (1-5M, bisulfite, or at least a supersaturated solution of Sodium Bisulfite) for conversion, maybe such that it will screw up the binding ability of the DNA to the SPRI beads. As it is salt and pH dependent.

 

Without having done it myself I am only hand waving.

 

N


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#3 hiri

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Posted 10 August 2015 - 05:02 PM

et2b,

 

I am curious if you've tried to do bisulfite conversion with the AMPure beads.. I tried once and the bisulfite solution turned yellow (presumably because of the beads?) and I'm too scared to move forward with this mess :-( 






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