Enrichment + bisulfite conv + amplification + seq

[Jessica.Ispada]

Hi there,

I want to enrich my samples with MethylMiner™ from invitrogen. And I also want to use one bisulfite conversion kit followed by whole genome amplification.
My question is, if after the enrichment my DNA is fragmented, can I proceed with the bisulfite conversion and genome amplification? Could I have problems with the amplification because my DNA is fragmented?

Many thanks!

[frozenlyse]

Isn't there already an amplification step after the enrichment (with primers against the Illumina adaptors which were ligated prior to the enrichment)?

[Jessica.Ispada]

Yes, but this amplification is to add the index 1 and index 2 required for cluster generation and sequencing. This step is not to increase the among of DNA. I work with embryos from different stages and sometimes I have embryos with just 2 cells. This is why its so important increase the amount of DNA after bisulfite conversion.