Fig. 3

iPS-microglia 2.0 are distinct from CD14⁺ and CD16⁺ monocytes Microglia differentiated using our published protocol are distinct from CD14⁺ monocytes and CD16⁺ inflammatory monocytes. In order to ensure our iPS-microglia 2.0 are similarly distinct from monocytes, differential expression analysis was computed with DEseq2. a Volcano plots of differentially expressed genes comparing genes enriched in CD16⁺ monocytes (pink) with genes enriched in iPSmicroglia 2.0 (dark blue) or iPS-microglia (light blue) show many significant differences between monocytes and microglia. Venn diagrams and comparative fold change plots of differentially expressed genes show that the vast majority of differences are identical between iPS-microglia and iPS-microglia 2.0 when compared to CD16⁺ monocytes. Direct comparisons of the fold change expression level (TPM) of every gene are shown in comparative fold change plots which demonstrate the striking similarity of differential expression when iPS-microglia and iPS-microglia 2.0 are each compared to CD16⁺ monocytes. b The same is true for comparisons of iPS-microglia and iPS-microglia 2.0 with CD14⁺ monocytes (purple)