Whole transcriptome differential analysis revealed increased expression of 1957 genes and 1071 genes in iMGLs when compared to Fetal MG or Adult MG, respectively. We also observed decreased expression of 1916 genes compared to fetal MG and 1263 genes compared to Adult MG. Enrichment analysis between iMGLs and primary microglia show that iMGLs are enriched for pathways involving cell cycle processes, migration, microtubule cytoskeletal organization, and inflammatory response, but do not differ in core myeloid GO terms (Tables S4–6). These terms reflect expected processes in which iMGLs are cued to respond to the environment and possess a capacity for renewal and maturation that have previously been reported in cultured microglia (Butovsky et al., 2014). Differential analysis between Fetal MG and Adult MG identified pathways related to responses to environment like migration and phagocytosis regulation, but not key myeloid genes in Fetal MG. Adult MG enrichment includes ECM organization, nervous system regulation, cell adhesion, and negative regulation of cell proliferation.
