WGA in MeDip-Seq

[mugiu17]

Hi!

I am planning to perform MeDip-seq experiments. Based on my samples, I plan to recover very little amount of methylated DNA. Therefore, I was thinking to perform an amplification step on the immunoprecipitated material before adapter ligation and gel size selection. Has anybody experience in some method of amplification that minimizes the introduction of bias in the experiment?

Thank you very much!

MGiulia

[yoon]

hello,
WGA is not really possible after DNA have been fragmented! Also, Medip usually yield ssDNA which is not possible to be ligated with illumina adapters.

[frozenlyse]

hello,
WGA is not really possible after DNA have been fragmented! Also, Medip usually yield ssDNA which is not possible to be ligated with illumina adapters.

So I would suggest you ligate on adaptors before the MeDIP - however the TruSeq adaptors you get from Illumina at the moment are methylated themself (apparently) so you need to get hold of/synthesise unmethylated adaptors.

[mugiu17]

Thanks for your answers!

I think that you can use WGA after MeDIP...for example look at http://www.nimblegen.com/products/methylation/tutorial/.
Moreover, I've found this product:

http://www.rubicongenomics.com/products/ipplex

These methods have been used MeDIP-Chip analysis, but I have not found any example in MeDIP-seq.