I'm going to study a TF and to save money and time I'd like to perform CHIP and CO-IP in the same reaction. At the end of the IP, I'd like to separate DNA from protein complex and study them independently. This approach can make sense? Or CHIP and CO-IP are completely incompatible?
Thanks
You mean separate protein/protein complex from DNA/protein complex before adding the beads ?
cause if so I don't think it is possible, I know no protocol able to separate those fractions considering you have protein in both fractions.
Usually we do CO IP with native conditions (no cross link) and weak salt concentration
but that's a good question i always wondered if we could mix these two technics
1.How do you separate DNA from protein complex? or you just divide your sample after IP into two pieces and then treat them separately?
2. what's your starting cell number? as far as I know,we do co-IP without crosslinking which is different from the X-ChIP(when you want to study the TF ,you have to crosslink to strengthen the TF and it's DNA binding )
3.I think your idea is good ,but my suggestion is that if your cell is sufficient and easy to get ,maybe you can perform these two experiments separately because there is some difference in these two steps.
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