Extended Data Fig. 1: Culture purity and lipotypes (most differentiating species) of human iPSC-derived neurons, astrocytes and microglia.

a) Representative image of iNeurons used for purity quantification. White circles in the right panel indicate ring region around automatically detected intact nuclei where MAP2 intensity was measured. Scale bar = 50μm (BIONi037-A parental line). b) Percentage of MAP2 positive cells. N=3, three independent experiments. Mean c-d) Representative images (c) and quantification (d) of the percentage of Vimentin or AQP4 positive ApoE3 and ApoE4 iAstrocytes. N=4 two independent experiments from two isogenic sets. Mean. Scale bar = 50μm. e) Representative flow cytometry plots showing that >97% of cells generated from the EB differentiation protocol are pre-macrophages that are then plated for final differentiation to iMicroglia. f) Representative images of differentiated iMicroglia (day 14). Scale bar = 50μm (BIONi037-A parental line). g) Relative mRNA expression levels determined by qPCR of indicated microglial genes at 0-14 days of differentiation from pre-macrophage stage. N=3, three independent experiments. Mean + sem. h) Heatmap of most differentiating lipid species different between iPSC-derived neurons, astrocytes and microglia. alpha = 0.8 is used for discriminant analysis.