What happens to DNA methylation when cells are in metaphase?

The reason I'm asking this is because I want to find out whether we can use FACS to isolate chromosomes and for next generation sequencing without having to sequence the whole genome...

Cheers

that is a good question and I don't think anyone knows.

one would assume by metaphase the copying of epigenetic information post S-phase is complete, so nothing happens to it at metaphase.

Thanks for your reply Nick. I've decided to go for another technique: sequence capture arrays. Novel and exciting :-)