downregulation of GATA 3 by shRNA's - (Nov/23/2008 )

Hi everyone,

To test if my plasmid vector with a shRNA against GATA 3 works. I've transfected my plasmid in HEK-T cells to see if the expression of GATA 3 is downregulated.
I've did a real-time PCR and compaired the expression of GATA 3 with actin and with GAPDH. The strange thing is that it seems better downregulated when compaired with actin than with GAPDH. Does anyone know how this is possible?

This may just reflect the quality of different internal controls: which gene was not least affected by the transfection. I tend to trust the actin result more because GAPDH has many pseudogenes that tiny contamination of DNA in your sample may interfere GAPDH level if its primers are not appropriately designed.