Supplementary Figure 1

Thestage2co-cultureofhumaniPS-MGandtheastrocytefeederlayerswereanalyzedbystainingwithENTPD1(CD39).

Co-cultures of human iPS-MG and the astrocyte feeder layers were analyzed by staining with ENTPD1 (CD39), a cell surface protein specific for microglia (right). Isotype antibody (left) was used as a control. Data is representative of two different differentiation experiments.

Nature Neuroscience doi:10.1038/nn.4534

Supplementary Figure 2

GeneExpressiondataextractedfromthehumanmicroarrayforthesixmicrogliaspecificgenes.

Our iMG show high expression of all the six microglia genes whereas the macrophages (Mac) and dendritic cells (DC) exhibit high expression of only selected genes. Data is representative of three different differentiation experiments.

Nature Neuroscience doi:10.1038/nn.4534

Supplementary Figure 3

Thestage2co-cultureofmurineiPS-MGandtheastrocytefeederlayerswereanalyzedbyGFP+cellsorting.

The iPS-MG were differentiated from CX3CR1-GFP+ iPSC cells. The CX3CR1 gene is specifically expressed in microglia, and hence the iPS-MG express GFP and can be conveniently separated from the co-culture through FACs sorting. Data is representative of three different differentiation experiments.

Nature Neuroscience doi:10.1038/nn.4534

Supplementary Figure 4

miPSCcellsgenerated fromCx3cr1gfp/+knockinmouseembryonic fibroblastsdemonstratepropertiesof identity,authenticity,andpluripotency.

Cx3cr1gfp/+ iPSCs stain for alkaline phosphatase (a), express the stem cell markers Oct4 (b) and Sox2 (c), form teratomas (d), can be used to generate chimeric mice (e), and display a normal karyotype (f). Data is representative of three different cell-culture for the alkaline phosphatase and immunocytochemistry experiments and 4 mice for the chimera experiments.

Nature Neuroscience doi:10.1038/nn.4534

Supplementary Table 1

Experimental groupings for the glioma tumor study

Nature Neuroscience doi:10.1038/nn.4534