Fig. 3

Functional characterization of cerebral organoids. a Co-expression patterns of DEGs with genes expressed in excitatory and inhibitory neurons. b Overlap of upregulated and downregulated DEGs with genes expressed in excitatory and inhibitory neurons. c, d Visualization and quantification of ER–mitochondria-associated membranes in cortical neurons, using PLA assays conducted with antibodies against VDA1 and IP3R. PLA spots indicting physical association between VDAC1 and IP3R are shown in green, neurites are stained with MAP 2 (white), and nuclei are stained with DAPI (blue) (× 60 magnification; scale bar = 20 μm). The mean numbers of PLA spots were calculated for the nuclear area and the neurites. Values are shown as mean ± SEM. Unpaired Student t test with Welch’s correction: ***p = 0.0004 and *p = 0.04. Eight CON lines were compared 8 BPI lines for this analysis. e Quantification of raster plot data collected before and after electrical stimulation with 0.8 V. f Quantification of raster plot data collected after depolarization with 30 mM KCl. Data was collected for four CON and four BPI iPSC organoids, with two technical replicates in each condition. Values are shown as mean ± SEM. Unpaired Student t test with Welch’s correction: ***p < 0.001 and **p = 0.0037