I am trying to determine the sex of de-identified mouse placenta and fetal liver RNA / cDNA. Unfortunately, I do not have to tissue left to genotype the samples. I ran qPCR using a probe for two different sequences of the SRY gene, and the cycle counts were all either high (35+) or undetermined for the placenta. For the livers, a majority of my samples registered as having low cycle counts for both SRY probes, which I found quite unlikely considering the statistical chance of nearly all my samples being male... this leads me to believe that the samples were somehow contaminated by human SRY mRNA or the mixed-sex litter in utero led to some sort of trans-placental contamination of mRNA if that is possible.

Are there any other genes that I could try, such as X-chromosome specific genes that are doubly expressed in females and low in males? Or perhaps another Y-chromosome specific gene? I need to find something obvious that is highly expressed in male liver/placenta or vice versa that will clearly allow me to determine the sex of the mouse my mRNA samples came from.