Monocyte-derived alveolar macrophages induced by influenza infection confer long-term antibacterial protection [RNA-seq 2]

To investigate transcriptomic differences using RNA-seq. This was done in macrophages isolated from a busulfan chimera, using congenic markers (CD45.1 for a BM origin, and CD45.2 for a host origin) in influenza-experienced, and naive lungs - at baseline and following Pam3CSK4 stimulation Overall design: In this experiment we sorted alveolar macrophages from naïve, and post-influenza mice using congenic markers to indicate origin. Cells were then stimulated ex vivo for 16 hours with Pam3CSk4 to investigate differences in stimulated cells, but also at steady state (Mock stimulated). This was done in parallel with ATAC-sequencing, to identify changes at both the transcriptional, and chromatin level in the same cells.