Fig. 5

Microwell geometry modulates gene expression programs related to neural cell type and brain region specification. A–d n = 3 biological replicates for each condition with 4–10 hCOs in each replicate. a Venn diagrams showing the differentially expressed genes with FDR p-value < 0.05 and log₂ (FC) ≥|1.5|. Boxed genes are the unique and common transcripts in each comparison with FDR p-value < 0.05, log₂ (FC) ≥|2| and max mean RPKM ≥ 5. b The number of differentially expressed genes across all microwell geometries with FDR p-value < 0.05 and log₂(FC) ≥|1.5|. c Differentially expressed marker genes between individual microwell geometries and round microwells with FDR p-value < 0.05. d Top biological functions between individual microwell geometries and round microwells with z-score ≥|2| and FDR p-value < 0.01 identified through IPA analysis. Differentially expressed genes with FDR p-value < 0.05, log₂ (FC) ≥|1.5| and max mean RPKM ≥ 5 were used in this analysis. 149 (Butterfly), 28 (Peanut) and 35 (c) genes met this criteria in day 10 hCOs. 286 (Butterfly), 266 (Peanut) and 88 (c) genes met this criteria in day 20 hCOs. 106 (Butterfly), 69 (Peanut) and 10 (c) genes met these criteria in day 40 hCOs