I am trying to work out a ChIP experiment. After my ChIP experiment, the DNA I am getting in INPUT is showing problem with amplification. In an RT PCR experiment when I am taking 1ul of this INPUT DNA, It shows a CT value of 36. While on increasing the volume of INPUT dna to 4ul in RT PCR, it does not even get amplified in 40 cycles.
I am using diagenode Ipure kit for DNA isolation (it is working fine in my other experiments). Problem persisted even when I have purified this INPUT DNA with agencourt amp pure beads. I have repeated the experiment 2 -3 times with same results.
Any suggestions !!