genome bisulfite sequencing

[luckylove]

Hi, could you give me some articles about genome bisulfite sequencing? Also, I have one question to ask:
When do genome bisulfite sequencing, there must to do two samples which is used to bisulfate treatment and the other used to control. Now I want to know how to choose the control. Is it the same sample as bisulfate treatment or not? For example, if I want to do bisulfate sequencing about human disease, should I use the patient DNA which don’t proceed bisulfate treatment as control or should I choose healthy person’ genome DNA as control? Thank you!

[simonandrews]

There's no intrinsic need for two samples in a BS-Seq experiment as long as you have a reference genome to map against, it depends on what biological question you're trying to address. There is potentially some value in taking the genotype of the individual you're working with into account when doing your BS-Seq mapping so you don't end up confounding genomic changes with methylaytion changes - but given that methylation changes generally extend over a wider stretch of DNA then you can normally remove abherrent methlyation calls by requiring a consistent change within a region and discarding single anomalous calls. For larger genome rearrangements you can still get away with using a common reference since any deletions or duplications will simply show up as changes in coverage, but this won't affect your methylation calls since these are calculated individually at each base.