Extended Data Fig. 1 |. Third-party comparison of different brain organoid protocols and the fetal human brain.

(a) Schematic View of the Culture System Generating human cortical organoids (hCOs). Guided protocols originated from Eiraku et al.⁵ while non-guided protocols are from Lancaster et al.¹⁹. Timeline of neural induction, differentiation, and maturation step is shown across protocols. Note that, while we have use the term ‘semi-guided’ here to describe our protocol and distinguish it from other Eiraku et al.⁵ -derived directed protocols, all panels in this figure are adapted from ref. 8, which only utilized the terms ‘guided’ and ‘unguided’ and thus correctly classified our protocol⁷ as guided. (b–d) Shared-nearest-neighbors (SNN) graph visualization for differentiation trajectory. (b) Differentiation directions (arrows) were determined by pseudotime. (c) Estimated trajectory backbone from the SNN graph. (d) Comparison of differentiation trajectory among different protocols. (e) The presence of cell types in each organoid protocol and human fetal brain. Cell types with >0.25% of cells are denoted with a plus sign. F, Fiddes et al.¹⁷; V, Velasco et al.⁶; B, Birey et al.¹⁴; M, Madhavan et al.¹⁸; T, Trujillo et al.⁷; X, Xiang et al.¹⁵; Q, Quadrato et al.²⁰; G, Giandomenico et al.⁵⁰. (f) Enrichment of disease-related genes in each organoid protocol. The red boxes indicate data generated from the protocol presented here. Figure adapted with permission from ref. 8, Elsevier.