Multiplexing ChIP-seq

[Giles]

I am aware of two Illumina kits that can do multiplexing: the "multiplexing sample preparation oligonucleotide kit" and the "TruSeq sample preparation kit". The steps between these procedures and the "ChIP-seq sample preparation kit" are qualitatively the same. However, it seems that the former two kits are designed for sequencing efforts that allow for large starting quantities of DNA (1-5ug). For ChIP-seq, you will be starting with more like 10ng.
The question is, has anyone done multiplexing for ChIP-seq? If so, which kit did you use? And, did you tweak the final concentrations of any of the steps to prevent a massive excess of adapters during the ligation?
Keith.

[csquared]

Keith,

We do it all the time with a custom kit that has some advantages to the TruSeq. Drop me a line and I can fill in the details. If you want to use the TruSeq kits, follow the protocol as written and just dilute the adaptors down 1:10 before ligation. All other steps can remain the same. The excess primer in the PCR isn't a problem.

Shawn

[Giles]

thanks for the info. That is exactly what I would have thought, but was hoping to get some confirmation.

[ETHANol]

http://seqanswers.com/forums/showthread.php?t=13093

I've prepared several libraries using this protocol and it works great.

csquared, I (and I bet others) would be interested in knowing the details. How about post it here.