Sample Prep Yields

[Giles]

I have recently gone through the generation of a ChIP-seq library using the standard Illumina protocol. According to this, I have done two gel purifications, one immediately following the adapter ligation and one immediately following the final library amplification. The library generation seemed to work, as I was able to see bands in the desired size range, however after the final gel purification I was lucky if I had 1ng of total DNA. This is far below what the core facility likes to have (~50ng).
I would love any stories/solutions that anyone can share regarding how much DNA they typically get back? Do you do two gel purifications? How many PCR cycles in the library amplifcation (the protocol calls for 18 cycles, but I have some colleagues that claim 25 is needed).

[epistatic]

If the ChIP DNA is sheared in a tight size range with the Covaris I avoid doing any gel purifications. I just had to be sure to adjust the adapter concentration for the lower than standard ChIP input to avoid adapter dimers.

If you can confirm the final library size with the HS bioanalyzer ChIP and have enough concentration to make a 10 nM stock for cluster generation, you should be good to go.