Dear Tina,

The equation used:

Delta Ct =CtSOI - CtRS; 

The value of Ct  is specific to the sequence of interest (SOI) and correspond to the number of cycles to reach a define threshold.

Whereas, Delta Ct corresponds to the difference between CtSOI and Ct of the reference sequence (RS), a house keeping gene sequence usually.

Delta Ct shows the difference of expression between 2 genes whereas Ct is specific to the expression of one gene.

Calculations using the  ∆∆Ct method:

1. Calculate ∆Ct (GOI - HKG) for each sample.

2. Average the  ∆Ct values for responders and non-responders.

3. Calculate the  ∆∆Ct ( ∆Ct responders -  ∆Ct non-responders).

4. Calculate the fold change using 2^- ∆∆Ct.

For more details, please see  attached file.

Hoping this will be helpful,

Rafik

 Dear Rafik,

Thank you so much for quick response. I do understand the comparative expression analysis method, and I have used that for ChIP-qPCR, however, in my expression analysis experiment I do not have a calibrator or non-responder if you like. I just want to see the expression level of GOI in different tissues under study. So I cannot use fold change method. Neither do I wish to consider any tissue as a control. These are WT-normal healthy plant leaf tissues and I am simply asking the question what is the expression level of x-gene in y-tissue for example, and I want to know if I could show 2^( -∆Ct) on the y-axis.

Thanks,

Tina