Figure 1

In vitro polarized macrophages display distinct M1 and M2 phenotypes. (A) Schematic of experimental design, where each point represents a collected sample, and each colored trajectory represents a different treatment condition. Murine bone marrow-derived macrophages were treated with cytokines to induce polarization (IFN-γ + LPS for M1, IL-4 for M2); M0 was maintained in base media as an unpolarized control (n = 3). (B) Multidimensional scaling (MDS) plot of RNA-seq expression (averaged across three replicates for each sample); points representing each sample are connected in order of collection, with point size representing the time spent (in hours) in culture. Macrophages treated with IFN-γ + LPS (M1) and IL-4 (M2) follow distinct polarization trajectories. (C) Gene expression in log(FPKM) of iNOS (a marker gene for M1 polarization) and Arg1 (a marker gene for M2 polarization) over time. (D) Jensen–Shannon distance (JSD) between the RNA expression profiles of M1- and M2-polarized macrophages and the 0 h M0 control. As a baseline for expected global expression differences between samples, the teal line shows the average JSD between all later M0 controls (collected at 24 h, 48 h, and 96 h) and the original 0 h M0 control sample.