Folding change by 2^DDCT method
I am doing a set of experiments to investigate if a gene knockout influences Virus replication. Briefly, we infected wild type cells and siRNA transfected cells and we achieved more than 90% of gene silencing. Now I want to quantify viral RNA inside the cells (not the Virus outside the cell). So that we have two Groups: Wild-Type and siRNA silenced.
I ran Real Time PCR for my target gene as well as Beta Actin as a reference gene. When I Analyse the data using the 2^(ddCT) (meaning 2^(ct ref-ct target)) I get really strange values.
Simply my question is: how to estimate how many times my gene is downregulated in comparison to WT?
For example , the wild type gives values of 0,0358 and the siRNA silenced cell 0,0019.
Could anyone help me with kind of analysis?
Thank a lot