Using qiagen kit for ChIP DNA purification - (May/27/2005 )
I use Qiagen PCR product purification kit instead of phenol-chloroform after reverse crosslinking crhomatin. Is it a good idea? Does anyone has any experience with using this kit for ChIP?
I thought of using it too, but have not because of uncertainty. Please let us know if it works.
I did use QiaEx II gel extraction kit for ChIP.
First of all, I have to mention that I still haven't solved the unspecific bands in No AB ctrl issue. In order to follow another person's protocol, who used the Ab that I am using, I religously followed his way of purification as well, which is P/C/I. The result is: the result of the purification methods didn't seem to differ.
I start with 10-20 million cells. And decross link only 1/3 of the input. One thing about using the QiaEx to clean up is using 5 ul of the beads for IP samples and 10 ul for Input ctrl.
Hope it helps those of you who want to save time
Thanks for sharing your result.
How many PCR cycles do you usually run for your Ab and no-Ab samples? If too many cycles are used, anything may turn positive. I would say keep the number of cycles below 30.
I think I may need to optimize the cycle numbers. Thanks for your suggestion