Extended Data Fig. 7: Comparison of patterning variability in the presence and absence of morphogen treatment.

a, PCA projection of summarized control samples colored by cell line of origin. Each dot represents one pool of 4-16 organoids from the same line that were exposed to a certain morphogen treatment in each experiment/batch. b-d, Bar plots showing last passage number, days in culture, total passage number (top) and stacked barplot showing proportion of cell types (bottom) for each experiment for HES3 (b), WTC (c), H9 (d). The bottom line indicates the month when each experiment was conducted. T1-3, Timing experiments 1-3; C1-4, Concentration experiments 1-4; O1-2, Combination experiments 1-2; C/O, Concentration and combination (mixed) experiment; GT, Gradient Timing experiment (data not shown); e, Schematic indicating the medium change regime for each experiment. Black cells indicate a medium change event. f, PCA projection of summarized control samples colored by medium change regime (as indicated in e), date of aggregation, last passage number, days in culture, plating dilution, split or thawn hSC source. Each dot represents one pool of 4-16 organoids from the same line that were exposed to a certain morphogen treatment in each experiment/batch. g, UMAP projection of summarized experiments, with each sample colored by cell line of origin. h shows the same projection but only control samples are highlighted for each cell line. i, UMAP projection split by morphogen identity for BMP4, BMP7 and FGF8 concentration experiments, colored by cell line of origin. j, Cell type composition of neural organoids exposed to increasing concentration steps of BMP4, BMP7 and FGF8 (late exposure, from day 12 to 21). Top, WTC organoids, middle, HES3 organoids, bottom, H9 organoids. Cell type colour legend is identical to b-d.