GSM7967325: Pdgfra-lineage - bleomycin day 14; Mus musculus; RNA-Seq
Lineage-traced cells were sorted by gating DAPI-, CD45-PeCy7-, CD31/326-APC-, tdTomato+ populations. The tdTomato+ cells were then loaded onto the 10x Chromium (10X Genomics). Epithelial and endothelial cells were sorted by gating DAPI-, CD45-PeCy7-, CD31/326-APC+. Immune cells were sorted by gating DAPI-, CD45-PeCy7+. Immune cells were then spiked back in with the epithelial and endothelial cells at a concentration of 25%. The resultant epithelial, endothelial, and immune cell mixture was then loaded onto the 10x Chromium (10x Genomics).  For the whole-lung scRNAseq presented in Figure 6, mouse lungs were digested and single cell suspensions were prepared as described above. Cell suspensions were then incubated with magnetic CD45 microbeads (Miltenyi Biotec, 130-052-301) for 30 minutes on ice. Cells were then passed through a magnetic column (LS column, Miltenyi Biotech) to deplete the cell suspension of CD45+ immune cells. CD45+ immune cells were then later recovered and spiked back into the CD45-depleted cell suspension at a concentration of 20%. The resultant cell mixture as then loaded onto the 10x Chromium controller. All samples were loaded to aim for a recovery of 10,000 cells, and libraries were prepped according to the manufacturer's protocol using the Chromium Single Cell 3' v3 chemistry. Libraries were then sequenced on an Illumina Novaseq 6000 instrument.