While calculation of the fold change expression of a transgene/gene, the expression level of target gene is normalize by subtracting delta Ct of treated sample with delta Ct of control sample. Suppose, one wants to evaluate fold change expression of a transgene in transgenic plants exposed to 50, 100 or 200 mM NaCl stress. A native homolog of the transgene exists in the transgenic plant (eg. AtCBF3 & LeCBF3). In this case, Ct Value of which plant sample we should choose to normalize the expression of transgene. Ct of Non-transgenic plant exposed to respective salt stress (Control) or Ct of transgenic plants exposed to 0mM (control)?

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