I have used the Cdh16-cre mice hybridizing with the X gene-flox mice to generated a tubular epithelial cells-specific X gene deletion mice. There was no problem with the genotyping, the cre was positive and the flox was homozygous. In addition, PCR on the kidney at gomomic level, in which the primer was designed to span the deleted sequence, showed a clear deletion of X gene.

Then i used the qRT-PCR to verify the X gene kockout efficiency of the kidney, and it showed that the X gene mRNA decresed significantly compared with the WT mice(the CT value of CKO mice was 22, while in WT mice it was 19 ), but the Westernblot (two types of antibody were used) and IHC showed that there was no difference in X protein( which is a secretory protein) level between the two types mice.

what might be the cause of this result? Thank you for helping me.