library_construction_protocol: We performed syngeneic orthotopic murine left lung transplants from CD45.2+ C57BL/6J to CD45.1+ C57BL/6J mice with 60 minutes of cold ischemia at 4˚C then 45 minutes of warm ischemia at 28˚C. Lung grafts were collected at various time points after reperfusion including 2 hours (WT2H), 3 days (WT3D), 7 days (WT7D), and 30 days (WT30D). Additionally, we collected single cell suspensions from naïve C57BL/6J left lungs (CTRL). For each sample (CTRL, WT2H, WT3D, WT7D, WT30D), we pooled cells from two lungs and sorted recipient CD45.1+ cells, donor CD45.2+ cells, and stromal CD45.1- cells. We then performed single-cell RNA sequencing on these samples. Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics