Unusually high yield with ChIP?

[lterhune]

Hi all,

A few days ago I completed a ChIP experiment from 10^8 cells that yielded a whopping 2.5ug of DNA at the end! The input (whole cell lysate) had about 3.5ug. This experiment has been validated with one of our collaborating labs, as well as myself back in the Fall. Both of us were used to getting 20-50ng total for library preparation. I'm wondering if one of the reagents went bad, such as the BSA solution for blocking, or any ideas about what could have happened. That much DNA just seems way too suspicious. Thanks!!

I will repeat this experiment regardless but would rather make an educated guess before going through more cells and reagents.

[xiaogao]

Hi，I think 10^8 cells were too much for each ChIP assay. I usually use 5X10^6--1X10^7 each ChIP. And also 20-50ng ChIP-DNA were got. So I do think 2.5ug ChIP-DNA was a bad result. Did you have detected the enrichment of your experement by RT-PCR?
Based on my experience, the ropiness of your sample or beads which were used for ChIP would lead to this result.

[nisha barak]

How did you measure your DNA concentration? Do you use a tRNA carrier? If so its possible this is inflating your reading. Finally have you tried running your input or ChIPped sample on a gel to verify that it looks like an unusually high concentration?