To define the molecular profiles of organoids, RNA-seq was performed in early (day 30) and late (day 72) stages of hMGEOs and hCOs as well as the parental hESCs. By comparing with published transcriptomes of 21 different human organs (Mele et al., 2015), we confirmed that hMGEOs and hCOs had the highest correlation with transcriptomes of human brain tissues (FDR<0.001) (Figure 4A). GO analysis revealed that multiple sets of neural development-related genes were significantly up-regulated in hMGEOs and hCOs after day 30 with pluripotency genes down-regulated (Figure 4B). Genes related with dendrite development, synapse organization, ion channel activity, and neurotransmitter secretion were similarly up-regulated in hMGEOs and hCOs at both time points. On the other hand, more developed hCOs displayed significantly higher expression of genes for neurotrophic signaling and calcium ion transport (Rutherford et al., 1997; Simms and Zamponi, 2014). Importantly, hMGEOs and hCOs displayed differential regulation of genes related to cell fate commitment (Figure 4B).
