Fig. 3

Brain organoids grown using microplate inserts show cerebral cortex identity. a i. Schematic showing the distribution of neuronal differentiation markers in the brain cortex. ii. Schematic representation of brain organoid cultures using the different microplate inserts. Control refers to the condition without insert. iii. Representative sections of cerebral organoids grown using the microplate inserts. Each tissue contains neural progenitors (PAX6⁺), intermediate progenitors (TBR2⁺), and neurons (CTIP2⁺, Tuj1⁺, MAP⁺), with no significant differences observed in the cytoarchitecture of the cerebral cortex of the brain organoids grown under the different experimental conditions (i.e. with or without microplate inserts). Panels were made with cropped images (same size for all panels shown). Image’s intensity levels were contracted at the same extent for all individual channels, across all panels shown to increase visibility and maximize compatibility between original 16-bit range -microscope image output- and 8-bit range (RGB) for Figure preparation in Adobe Illustrator. Scale Bar = 100 μm b Heatmap of Spearman correlation analysis of gene expression between H9 and H9-GFP hESC, brain organoids (grown with and without microplate inserts), previously published organoid RNA-seq data [33] and BrainSpan database https://www.brainspan.org/static/download.html. Hipp-Amy: Hippocampus-Amygdala