I have recently done ChIP-PCR for several potentially new target genes of my TF which worked very well. Then repeated the experiment to use the DNA for Illumina Hi-seq, but first tested the ChIP for one of my targets with PCR, again with a good result.
When I sent my DNA to the core lab for sequencing, they said that the amount of DNA was very low (was to be expected) and they used the NEBnext ultra library prep kit which includes a PCR step for the library preparation. Samples were then sent to another core lab for the sequencing.
The results were quite disappointing: we couldn't find any relevant peaks, not even near the genes that I had used for PCR. Instead, there were a whole bunch of reads (about 10% in the input samples and about 30% in the ChIP'd samples) alledgedly coming from Plasmodium (my DNA was mouse), although now they believe that these are just repeat sequences coming from the mouse. Also, the input DNA doesn't look as if it's genomic DNA but really has distinct peaks.
My first guess was that they somehow swapped samples, but they say that's impossible. So my questions are, is it possible that some kind of bias was introduced during the library prep? How is it possible that we don't see any peaks near any of the known target genes of this TF, whereas we do see enrichment with PCR? Shouldn't the Hi-seq at least pick those up? They say that it may be because with PCR we are looking at very distinct regions which is not the case with sequencing, but I believe that's just BS.
Any thoughts please?