library_construction_protocol: Lungs were dissected and processed into a single cell suspension using Liberase TM and DNAse containing media and processed on a GentleMACs octodissociator. Cells were stained with a cocktail of fluorescently-conjugated antibodies to identify Macrophages with or without ingestion of ZsGreen. Cells were sorted directly into Arcturus Pico Pure Lysis buffer and RNA prepared using the Arcturus PicoPure RNA Isolation Kit. Libraries were prepared for each sample utilizing the Nugen Ovation Library Preparation Kit (Tecan). Single End 50bp sequencing was performed on an Illumina HiSeq 3000.