If the RBCs were lysed, then the RNA content from the RBCs is now in your serum samples. So yes, I would expect this to affect gene expression results. I think you should replace these samples.

Although the RBCs do not have nucleus, they still have some RNA inside that may contaminate your samples and besides, hemoglobin is known inhibitor in RT-PCR as it quenches fluorescence. So make sure that your samples are purified.

I would suggest purifying the PBMC first with Ficoll-Hypaque method before doing RNA purification.

@Don Ashley,

Please provide the procedure of purification by Ficoll-Hypaque method.