ChIP Kick

The Qiaquick kit from Qiagen works just fine with the millipore kit. I make use of the Millipore magna-chip kit as well and have run into the same problem. I wrote out all the ingredients that come with the kit and how many I use per ChIP sample (I'm dissecting out brain tissue, so I use different amounts than Millipore recommends) and which reagents are my limiting reagents. For me it was the Cell Lysis Buffer and the Protease Inhibitor cocktail.

Like you, I tried to order reagents individually, but they don't sell them; but if you call Millipore they will give you the composition of many of their reagents (e.g, now I make my own cell lysis buffer) or buy them from elsewhere (I've been using the Halt protease/phosphatase inhibitor cocktail from Pierce; has worked well so far). I think it's quite obnoxious that they don't sell components individually given that various labs have different reagent requirements....

MM

I did not do any experiment after above attempt.
What's the marker size in your case?  I have consistently observed that if u load the sonicated samples directly (without phenol purifyling and having 1% SDS coming from lysis buffer in my case) onto the agarose gel, you get some weared pattern. I am sure you have done the same. So my suggesiton is that after RNase-proteinaseK incubation give phenol-chloroform treatment followed by alcohol (isopropanol or ethanol) precipitation and than load the samples on gel for analyzing the size.