Hi, I'm planning to do MeDIP-PCR or qPCR, and it's first try in my lab so I need some help.

1) Most of the papers and protocols I found are using magnetic bead like Dynabead for IP.

Unfortunately, our lab doesn't use magnetic bead but use protein A or protein G agarose bead for IP.

Is there anyone who did MeDIP using agarose bead? Would it be okay to use agarose bead for MeDIP?

If agarse bead is not suitable to do MeDIP, can you explain the reason?

If it's okay, could you share the MeDIP protocol using agarose bead?

2) I'm searching for 5-methylcytosine antibody. I found that clone 33D3 antibody is widely used for MeDIP and so many companies are distributing clone 33D3 antibody. Is every clone 33D3 identical regardless of distributing company so I can just buy the cheapest one? Or is there anything else I should consider? (It would be thankful if you recommend 5-mC antibody for MeDIP)

3) I'm also finding a reliable control for MeDIP-PCR. My gDNA sample is from mouse spleen CD4 T cell. I'm considering to use GAPDH promoter region primer as a negative control, but I'm still looking for positive control. Is there any gene widely used as positive control? If there other negative control used widely, please let me know.

Thanks all!