Fig. 4

Comparison of individual microwell shapes to 96-well derived hCOs reveal shape specific differences in gene expression. A–c n = 3 biological replicates for each condition with 4–10 hCOs in each replicate. a Volcano plots of differentially expressed genes between individual microwell shapes and 96-wells at day 40. Red highlighted genes: FDR p-value < 0.05, log₂ (FC) ≥|2| and max mean RPKM ≥ 5. b Differentially expressed marker genes between individual microwell shapes and 96-wells with FDR p-value < 0.05. c Top biological functions between individual microwell shapes and 96-wells at day 40 with z-score ≥|2| and FDR p-value < 0.001 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. 174 (Round), 223 (Butterfly), 222 (Peanut) and 184 (c) genes met this criteria