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-   -   RRBS libraray prep options for NGS (http://seqanswers.com/forums/showthread.php?t=77638)

OUH-Seq 08-18-2017 03:52 AM

RRBS libraray prep options for NGS
 
We are trying to find the best option to sample prep 50 samples (cost effective, high data output) for methylation sequencing (RRBS) on the NextSeq500. We found 4 candidates that look interesting:
Bioo Scientific NextFlex
Diagenode RRBS premium
NuGen Ovation Kit
EpiNext High-Sensitivity Bisulfite-Seq Kit
Has anyone done a comparison or has tried one of these systems to talk to me about major disadvantages?

Thanks in advance guys
Greetings from Denmark

huguesparri 09-14-2017 05:35 AM

We have tested the Diagenode kit with success (24 reactions).
For me the biggest issue is that the kit do not provide a lot of reagents in excess.
And as you have to pool you samples before the bisulfite convertion, you are more or less forced to stick to their multiplexing design.

nucacidhunter 09-15-2017 02:27 AM

Among those NuGEN kit is innovative and allows direct ligation of restriction overhang compatible adapters to restriction fragments. The downside is that around 75% of index sequences can be identified wasting 25% of reads but it does not require addition of high PhiX% as library is high diversity.

luc 09-18-2017 08:14 AM

The Diagenode kit works fine but is quite laborious -- e.g. intermediate qPCR steps. Sorry we have not done any comparisons.

Diagenode 09-18-2017 12:05 PM

Hi huguesparri, that's great you have tried Diagenode Premium RRBS kit successfully. We offer some separate components for this kit. Please visit our website www.diagenode.com to check more or consult with our Technical Support should there be a separate reagent needed which is not listed. We will be happy to provide one so that you continue your experiments with success.

huguesparri 09-19-2017 04:44 AM

Quote:

Originally Posted by Diagenode (Post 211034)
Hi huguesparri, that's great you have tried Diagenode Premium RRBS kit successfully. We offer some separate components for this kit. Please visit our website www.diagenode.com to check more or consult with our Technical Support should there be a separate reagent needed which is not listed. We will be happy to provide one so that you continue your experiments with success.

Thanks for the tip.
We'll keep it in mind next time we plan some RRBS experiment :)


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