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

To investigate differences in the chromatin accessibility using ATAC-seq. This was done in macrophages from a BM origin (CD45.1) and embryonic origin (CD45.2) 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 2 hours with Pam3CSk4 to investigate differences in stimulated cells, but also at steady state (Mock stimulated). This was done in parallel with RNA-sequencing, to identify changes at both the transcriptional, and chromatin level in the same cells.