Investigating the impact of cigarette smoke on pulmonary cellular immune responses to influenza virus at the single cell resolution in mice.

Single cell RNA-sequencing (scRNAseq) of lung immune cells from mice exposed to room air or cigarette smoke, infected with influenza A virus. Room air saline controls are also included. This analysis facilitates a comparison of cigarette smoke-associated changes to the pulmonary immune environment at the level of individual leukocytes and stromal cells. BALB/c mice were exposed to room air or cigarette smoke for two weeks, and subsequently infected with 50 PFU of influenza A/FM/1/47-MA (H1N1). Control room air-exposed mice administered saline were also included. Smoke exposure was re-initiated from 3-7dpi, and whole lung samples were sampled and sequenced at 7dpi. n=4-5 mice were pooled per group. Reads were aligned to mouse genome reference and A/FM/1/47-MA cRNAs (details below).