Bisulphite sequencing -pick clones - (Jul/18/2005 )

hi all,

I have treated treated genomic dna with bisulphite. after that, i cloned the amplfied fragments by TA cloning and did the sequencing. From papers, I usually saw people they picked 10 clones for each sample. I want to ask how many of the clones are found to be methylated , for example, out of 10 clones, to claim that region to be really methylated? is there any absolute value for that? for example, 5 out of 10? or are there any papers which show more details about this? Thx!!!!!!

Samantha

Hi samantha, usually if the region is hypermethylated, then all clones should be methylated. If you are looking at a imprinted DMR then you would expect 50% of your clones to be methylated and 50% that are not, representing both alleles.

There is no paper that I am aware of that looks at your issue. The more clones you sequence, the more representative you data reflect the population of cells you were looking at!

Nick