Fig. 3

Early microwell culture affects subsequent hCO neurodevelopment. a PCA of gene expression at individual time points. n = 3 biological replicates for each condition with 4–8 hCOs in each replicate. b, c n = 12 biological replicates for microwell device (all shapes) with 4–8 hCOs in each replicate, n = 3 for 96-well plate with 4–8 hCOs in each. b The number of differentially expressed (up arrow) upregulated and (down arrow) downregulated genes between microwell device and 96-well plate with FDR p-value < 0.05 and log₂(FC) ≥|1.5|. c Top biological functions between microwell device and 96-well plate with z-score ≥|2| and FDR p-value < 0.001 identified through IPA analysis. Differentially expressed genes with FDR p-value < 0.05 and log₂ (FC) ≥|2| associated with each function are highlighted. Differentially expressed genes with FDR p-value < 0.05, log₂ (FC) ≥|1.5| and max mean RPKM ≥ 5 were used in this analysis. 51 (day 10), 56 (day 20) and 166 (day 40) genes met this criteria