Analyzing host cell response using RNA-seq allows us to understand what is happening within the host cell that could be missed by narrower analysis. From the analyses in this study, we can broadly state that extracellular vesicles (EVs) produced by Staphylococcus aureus at different physiological temperatures have varying effects on host cell gene expression. Infection and immune system-related genes appear to be upregulated in THP-1-derived macrophages treated with EVs produced at 37°C (core body temperature). These genes then appear to be downregulated in macrophages treated with EVs produced at 34ºC (the temperature of the anterior nares, where S. aureus colonizes). This pattern observed with EV-treated macrophages was not observed in EV-treated human nasal epithelial cells (HNECs). By utilizing RNA-seq we can see on a global level how RNA introduced to human cells, via EVs or a future vaccine, has an effect on our own gene expression.