This study was done to show the utility of precision-cut lung slices (PCLS) in supporting the survival of Pneumocystis murina in vitro. Overall design: We cultured PCLS derived from wild type C57BL/6 and immunocompromised Rag2-/-Il2rγ-/- mice with a P. murina inoculum in submerged or air-liquid interface models for up to 14 days. We isolated total RNA from the cultured lung tissues at days 0, 3, 7, 10 and 14 and analyzed for the expression of host lung genes and P. murina genes (Gsc1 for asci and Sp for trophs) by real-time qPCR. We then performed gene expression profiling analysis using data obtained from RNA-seq of naïve and P. murina - inoculated PCLS on day 3 and day 14 of culture in comparison to in vivo P. murina infected mice on day 14.