After some consulting I decided to use a commercial pcr cleanup spin column kit to concentrate DNA from my CHIP for sequencing. The DNA was in elutate of sodium bicarbonate and 1% SDS. Instructions required me to dilute 6x in binding buffer, so this meant 9mL per sample column. When combined, precipitate came out, I assume this was the SDS. All of the protocols I've seen that use sodium biocarbonate and SDS to elute out dna jumped straight to purification using p/c or kits so I just moved on.

I ran the liquid through the column and near the end when I was washing them I noticed that the membrane of the tubes looked a bit crumpled and the wash buffer was dripping through it somewhat faster than in control columns and whitish precipitate was in the wash. I tried looking at the membrane at every angle but I didn't see any hole. After I eluted I noticed a tiny pellet of whitish stuff at the bottom of the tube. I'm not sure whether this was SDS or silica or what. I had the elutant tested through qubit and the samples showed very low to below threshold amounts of DNA. But this was CHIP pulldowns so this is not necessarily indicative that something is wrong. I was wondering what sort of steps I should take from here. Should just move on and see if I can create a library and do a PCR check or assume the columns were broken and try to reprocess the binding buffer waste which I kept? Multiple companies I contacted seemed to think that the spin columns should be able to withstand that volume although one of them (Thermofisher) apparently has columns with membranes that look thicker than the kit I was using.