MBD-Seq Help

[harishrk]

Hi,
We are planning to use the MethylQuest kit (Millipore) to generate samples for sequencing using the Illumina platform. Has anyone used this kit and if so is there something to keep in mind?
All the literature (as much as I could gather) on MBD-Seq uses the Methylminer kit and I am wondering if there is a reason for that. The end DNA is double stranded and so I do not have to attach the adapters before-hand and the samples can be processed as for Chip-seq, but other than that does anyone have any suggestions for effective MBD-Seq?
Does the MethylQuest protocol have to be modified in any way to achieve good sequencing depth? Also typically what controls are people doing for these kinds of analysis?
Thank you very much.

[ETHANol]

Sorry to hijack your thread a little but has anybody compared MeDIP-seq with a MBD-seq (Methylminer or MethylQuest kit)?

If anyone is interested, my take on MeDIP-seq is here:

http://ethanomics.wordpress.com/medip-seq-protocol-with-truseq-adapters/

[methylnick]

There is a paper on this already,

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Research 2010, 20(12):1719-29

[harishrk]

There is a paper on this already,

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Research 2010, 20(12):1719-29

Hi,
Subsequent to posting here we found this article too. Thanx for the reply.
Regards.

[methylnick]

no worries, I am a methyl miner user, so can't really comment on methyl quest