upregulated genes were enriched for synaptic transmission genes (GO enrichment, P = 0.009), whereas the downregulated genes were enriched for cell cycle (P = 0.02) and cell division genes (P = 0.001). We next used transition mapping12 to assess the similarity of the transcription transitions between in vitro development of the hCSs and two time points in the developing human brain. For this analysis we employed the transcriptional spatiotemporal atlas of the human brain13 and the laminar expression data dissected via laser capture microdissection from fetal human brain14. We found that the transition between day 52 and day 76 of in vitro development had the strongest overlap (max-log10(P value) > 83) with the ventricular zone (VZ)/subventricular zone (SVZ) and with the intermediate zone (IZ)/subplate (SP)/inner cortical plate (CPi), respectively (Fig. 1f).
