Which DNA strand is recommended - (Feb/11/2013 )
Since it is assumed that both DNA strands have the same methylation pattern, there is no need to sequence both of them.
But which strand is recommended to sequence? I've read that is easier to sequence the sense strand (using the reverse primer). It that correct?
Yes, DNA methylation is symmetric and the plus strand of DNA is usually examined.
If you use the plus strand to design primers, sequencing the resulting pcr product using either forward or reverse primer is always sequencing the plus DNA strand, not the minus DNA strand. In general, reverse primer works better than forward primer in sequencing reaction.