Identification and characterization of alveolar and recruited lung macrophages during acute lung inflammation

To precisely identify mice resident alveolar macrophages (AMs) and bone marrow (BM)-derived macrophages, we developed a technique to separately label AMs and BM-derived macrophages with a fluorescent lipophilic dye followed by fluorescent-associated cell sorting (FACS). We utilized this approach to isolate BM-derived macrophages and AMs at different timepoints after intratracheal (IT) instillation of E.coli lipopolysaccharide (LPS) and performed bulk RNAseq on these cell populations to characterize the individual phenotypes of resident AMs and BM-derived macrophages present in the lungs. Overall design: Comparative gene expression profiling analysis of RNA-seq data for BM-derived macrophages and resident AMs at day0, day1 day3,and day7 after IT LPS