I performed real-time PCR using an Applied biosystems machine. The double delta Ct values ( according to the machine) for the gene of interest after certain treatments were given as -5.12454; -4.93158 ; -9.11017. Does this tell me about the fold change in the expression of this gene? If Yes, then does this mean there is negative fold change or a positive fold change in the expression of my gene of interest?
The formula to convert a deltadelta-Ct to a fold change is :
2^-(deltadelta-Ct)
So in your case, you would get a fold change of +34.89 from your deltadelta-Ct of -5.12. A negative deltadelta-Ct gives a positive fold change (higher expression of your gene after the treatment).
Usually the machine can give you the fold changes directly. You might want to play with the parameters. Nonetherless, even with just the Ct values, you can manually do the calculations fairly easily.
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