Actually i want to know is it acceptable to get variation in expression of housekeeping genes like GAPDH and Actin which i am getting in Real time pcr? in normal condition actin's avg ct is around 16 and that of GAPDH it is around 20,, but avg CT of GAPDH gets change whenever i m trying to do Real time at different condition, its aroung 16 whereas for actin it is nearby 14..
It this change in Ct of control (Housekeeping genes) are acceptable?
The Ct values for GAPDH usually between the range of 15 to 22 ct depending on the cell types. The Ct value can vary since it depend on input cDNA you taken as sample for the reaction. GAPDH is high copy number gene so high Ct values can be expected. As always suggested that within technical replicates, the difference should not be more than 0.5 cycles and for biological replicate the value should be more than 0.5-1 cycle between assays for the sample.