Dear Maynak Chakraborty, you should not use diluted DNA, as it may complicate your calculations. You are not interesed in comparing raw DNA quantities / concentrations but enrichment in a particular sequence. Input and precipitate do not contain the same DNA, you have fragmented genomic DNA in the first case and DNA enriched in a specific fragment in the second case. As you used your input for IP, the only relevant factor is the dilution between your input and your precipitate (how much of each did you use, and in which volume did you dilute them after DNA purification). I usually run a qCPR with purified DNA as they are and with some dilutions (1/5, 1/10, 1/100...) to be sure to be in the right efficiency zone. Then I compare input and IP (both specific and control IgG) as for gene expression (2-DD(ct) method), taking into account all the dilution factors. That gives the percentage of input values. Then you divide %input(ChIP) by %input(IgG) and that gives the enrichment value. Hope that helps, good luck!

Thank you Fabrice.Before IP, i dilute my raw chromatin samples 10 times and take 1% of diluted DNA as input. After DNA elution and final purification, I take 3ul from each samples ( Input, IP and Mock) and run a qPCR. I think, I have to subtract 6.664 value from my input Ct to get its original Ct. Is the procedure ok for calculation?