scRNAseq of lungs from APOE knock-in mice with COVID-19

We performed single cell RNA-sequencing of lungs from APOE knock-in mice in the absence of infection or four days post infection with SARS-CoV-2 MA10. Infected mice showed major remodeling of the cellular composition with expansion of myeloid cells and relative depletion of epithelial cells. In infected mice, APOE2 mice showed enrichment of pathways implicated in immune activation, consistent with immunologic misfiring. Overall design: scRNAseq of lungs from APOE knock-in mice with or without COVID-19. Libraries were prepared with the whole transcriptome 100K kit from Parse Biosciences, which involves barcoding and then pooling cells from all samples prior to generation of eight sublibraries. Because of the design of the kit, sequencing reads of all samples are distributed across all eight sublibraries. For further details see attached `README.txt` file. Samples: ctrl_01_E2, ctrl_02_E2, ctrl_03_E2, ctrl_04_E3, ctrl_05_E3, ctrl_06_E3, ctrl_07_E4, ctrl_08_E4, ctrl_09_E4, inf_01_E2, inf_02_E2, inf_03_E3, inf_04_E3, inf_05_E4, inf_06_E4, inf_07_E4, inf_08_E2, inf_09_E2, inf_10_E2, inf_11_E3, inf_12_E3, inf_13_E4, inf_15_E4, inf_16_E4, inf_17_E2, inf_18_E3, inf_19_E4, inf_20_E4, inf_23_E3