Fig. 1

Mesodermal progenitors develop into microglia-like cells within cerebral organoids. a Schematic overview of the cerebral organoid protocol depicting the essential steps in the differentiation process. Embryoid bodies are formed (day 1–6) after which neuroectoderm is induced (day 6–13). Matrigel embedment provides an extracellular matrix to further grow and develop. Four days later they are transferred to a spinning bioreactor. Before matrigel embedment they have a smooth surface (i), which changes into a surface showing typical budding of the organoid 4 days after matrigel embedment (ii). Scale bar 100 µm. See also Supplementary Fig. 1, 2, and Supplementary Table 1. b AFP, PAX6, and brachyury immunostainings, which are markers for the germ layers endoderm ectoderm and mesoderm, respectively. Representative pictures of cerebral organoids are shown at an early stage of organoid development (day 17). Scale bar 40 µm. c, d Brachyury and IBA-1 immunostainings in cerebral organoids at 17 days (c), 24 days (c, d) and 52 days (c) in culture. Co-expression of IBA-1 and brachyury was visible at day 24. Scale bars 100 (c) and 40 µm (d). e IBA-1 immunostainings show distribution of microglia-like cells in cerebral organoids at day 31 and day 52 in culture. Scale bar 40 µm. f, g The perimeter of microglia at day 31 and day 52 quantified (f) with an automated approach by FIJI of IBA-1⁺ immunostainings of cerebral organoids (g). n = 4 images of organoids quantified per timepoint, Mann–Whitney test U = 0, p = 0.029. Data is represented as median. Scale bars 40 µm. (close-up and perimeter are shown) (*p < 0.05). h Morphology of microglia-like cells illustrated by IBA-1⁺ immunostainings after 66 days in culture. Scale bar 40 µm. (close-up and perimeter are shown) Representative pictures of cerebral organoids from iPSC 1 are shown