Have you figured your problem yet on low peak signal? Recently I have been in similar situations that couple of my histone ChIP and Anti-HA Tag ChIP are not working out quite well, and like you said resembling to those ChIP of inefficient antibody. I kind of in line with zhaoj who suggest that the ChIP DNA used for making library is not enough. Previously I chip-seq two samples, K4me3 and K27me3, both of them working out really fine, although I only use 1 millions cells for chip assay. I thought I could get similar success by using same number of cells for one transcriptional factor ChIP (HA tagged), and one histone ChIP (K79me2), however the sequencing results turned out are not good, e.g. not many peaks, and high FDR (30%). Similar to you, I am quite confident that the antibody should be ok, as I checked it by QPCR to show good enrichments on my known targets. While I am repeating the ChIP seq with more cells and waiting for the results, I wonder there could be other problems that cause the failure of ChIP seq?

For your bioanalyzer questions, I have tried the high sensitivity kit that can not detect the ChIP DNA, I guess because the quantity of ChIP DNA is really low, plus that they are in smear (not a single band), so even let's say if you have 5ng total but the smear may have 1000 bands, each band end up has 5pg, is already reach the limit of detection. In other aspect I guess all people using bioanalyser should pay attention is the bioanalyser is very sensitive to salt that means if there's minimal salt in your ChIP DNA that will ruin the measurement, I have seen this many times already, especially for phenol purified ChIP DNA which is not very clean and always contains a lot of salt. Hope this helps.

So you said you combined 2 ChIP assay DNA to make library which works, do you know that equal to how many cells? Dose your transcriptional factor bind to a lot of genomic targets? I found if a TF doesn't have many targets may require even more cells. Right now I don't even bother to measure the ChIP DNA as I think that can not guarantee the ChIP seq will work. Even you ChIP with IgG which can give several ng of ChIP DNA that will make a good library but not give you any significant peaks. Seems people more incline to use more than 10 millions cells for TF ChIP, while histone ChIP can be in million range.

In a previous experiment I used some MIRA enriched DNA (methylated) for a single read library prep (using Illumina Chip-seq kit) and sequencing, which worked very well. Right now I have lots of ChIP samples to sequence of various amounts (2-20ng). We decided we will use PE adapters for all sample preps from here on. I'm testing the NEBNext DNA sample prep kit and Illumina PE sample prep kits with different amounts of DNA (1-10ng). The question I have is whether anyone adopted the PE sample prep kit (where they use lot more reagents and enzymes) to the ChiIP-sample prep kit. Of course I will change the adapter and primer concentrations. I'm also testing TUFTS custom adapters and primers they they were gracious to share. Thanks in advance.