Using ddCt method to calculate the fold change in gene expression experiment and I don't know if i should go with SD,SE or 2SE(CI:95%) to calculate the range of values that the fold lies within
If you want to get a confidence interval, then use the approriate quantile of the t-distribution and the standard error (SE), as the 2-sided (1-alpha)*100% confidence interval is average ± t(1-alpha/2; d.f.)*SE where d.f. is the number of degrees of freedom used to estimate the standard error.