Next, we directly tested whether there was any bias for differentiation into specific neuronal subtypes. In this analysis, we used as markers TFs which control fate choice, cell proliferation, and neuronal differentiation during normal telencephalic development, many of which were members of the magenta and blue modules (Figure 2C; Tables S5, S6). We found that the proportions of cortical excitatory neuron precursors of the subventricular zone expressing EOMES/TBR2, of layer 6 neurons expressing TBR1, and of early-born layer 5 CTIP2 neurons (also known as BCL11B) were not significantly different in ASD and control organoids at TD31 (Figure 4A–F), although some of these cortical excitatory neuron markers (such as TBR1, TBR2, CTIP2 and SOX5) were upregulated in proband-derived organoids at the mRNA level.
