Dear All,

I have been trying to do ChIP qPCRs in Drosophila S2 cells to analyze the recruitment of a protein on certain genes. The problems that I am facing are- the yield is very low (0.001-0.005% of input); When I run the quality control samples after sonification on 1% agarose gels, I see a faint smear, Picture attached (sonification is done 2 times - 9 Cycles on & off, with 30 sec off using Bioruptor). Finally, my ChIP results are somewhat inconsistent, the intergenic regions which I know should not show the recruitment of my protein also show the recruitment after treatment. So, a brief on experiment- Before treatment there should be very little of my protein on target genes and after treatment this should increase significantly. I do see a little increment after treatment but same is happening in intergenic region. Also, my IgG control shows the same.

I would appreciate your help in trouble shooting.

Thank you

Ikram