Phenotypical cell percentages and total cell numbers for each well of each bioreactor in each set were collated into large matrices organized for input into Minitab. A general factorial analysis was constructed with four factors: input A (FGF9 or CHIR, 3 values), input B (BMP7 or AGN, 3 values), input C (RA, 3 values), and input D (row number/paracrine factors, 10 values). For each dataset, there were between two and four replicates. Data were randomized and transformed with a Box-Cox transformation (λ set to optimal), and subsequent normality was confirmed. Standardized Pareto charts were generated, and main effects plots were generated and adapted to fit on a single plot, while interaction plots failed to show clear or significant trends. Plots generated were shown in Figs. 4 and 6 and figs. S5 and S8.

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