Single-cell RNA-seq of control and Sendai virus-infected mouse lungs [1wk/7wk timepoint]

The Sendai virus infection model induces global changes involving multiple lung cell types. At 1 week post-infection, there is acute damage to the lung. At 2 weeks post-infection, when the virus had been largely cleared and the lung is undergoing repair, proliferation of endothelial cells and alveolar type 2 (AT2) cells is observed, as well as aberrant appearance Trp63/Sox2-expressing basal-like cells reminiscent of pods or lineage-negative epithelial progenitors observed upon severe H1N1 virus infection. At 7 weeks post-infection, the lung has been largely repaired, though the Trp63/Sox2-expressing basal-like cells remain. FACS-purified control or virus infected whole murine lung epithelial, endothelial, mesenchymal, and immune cells were mixed together in similar proportions and processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics). The samples GSM4293527 and GSM4293528 from GSE144678 are also included in this study.