A Single Cell Atlas of Alveolar Development

The later stages of lung development are defined by the structural processes of sacculation and alveolarization, with dramatic shifts in the spatial organization and function of epithelial, endothelial, and mesenchymal cells. To investigate the coordination of the cellular changes in the lung parenchyma during development we performed a single cell RNA sequencing time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14). We combined new computational analysis with RNA in situ hybridization to explore transcriptional velocity, fate likelihood prediction, and temporally and spatial localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of elastin assembly and demonstrate an integrated view of the cellular dynamics during later lung development. Overall design: Single Cell RNAseq of dissociated mouse lungs at ages: E12, E15, P3, P5, and P7. Suspensions were enriched for cells that were CD45 negative, Ter119 negative, and viable. P7 lungs were enriched for epithelial cells by collecting EPCAM positive cells.