I have checked for gender using PCR after extracting the DNA. However now the samples were processed and lysed for RNAseq already. So is there a way to check for gender now?
Do you mean before RNA-Seq or from the RNA-Seq data? I guess you could check for the expression of y-chromosome specific genes in the data, but then again, it depends on which tissue you use to do RNA-Seq from. Is it really the gender you are interested in? Because if it is just sample identity, you could also check for the mitochondrial markers. RNA-Seq usually contains a lot of reads to get a "mitochondrial fingerprint" which you could check lateron in your DNA samples...
Probably more information on what you're trying to do would help us to be more helpful to you
I believe that XIST mRNA is only expressed in females - you could qPCR for that.
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