Fig. 2: Cell type diversity in Hi-Q brain organoids across maturation.
A Force Altas (FA) 2D representation of the neighbor graph of Hi-Q brain organoids at different time points of development (Day 60, 90, and 150). Cells are colored according to the label with the highest score given by the Lasso logistic regression model trained on primary brain data31. B Histogram plot reporting the proportion of different cell types at different time points of development. C, D FA representation of the neighbor graph of the integrated datasets from all stages. In panel (C), clusters are annotated using the expressed gene markers: Pro-RG, proliferating radial glia; AP, apical progenitors; RG, radial glia; A/O, astrocytes, and oligodendrocytes; IPC, intermediate precursor cells; Dev-N, developing neurons; Dev-HB, developing hindbrain; EaN, early neurons; EN, excitatory neurons; IN, inhibitory neurons. In panel (D), cells are colored according to the time they were sampled. E The subset of the whole integrated dataset, except the pro-RG cluster, colored by pseudotime, showing the two trajectories of developing IN (green arrow) and EN (blue arrow). The scatter plots show the expression range of characteristic IN and EN genes for each cell in function of the pseudotime. F Violin plots compare the level of expression of PGK1, ARCN1, and GORASP2, as well as the cumulative score between Hi-Q brain organoids (nine organoids from three different age groups used in Fig. 2B), other brain organoids21,30, and primary data from the literature. The overlaid box indicates median, quartiles, and 1.5× IQR whiskers; outliers are individual points.
