Extended Data Fig. 1: Brainstem organoid specification and reproducibility.
a, Overview of patterning approach and corresponding representative brightfield images of brainstem organoids over time. n = 3 BrOs for early time points, n = 15 BrOs for timepoint 60 days, scale bar of single organoids and multiple organoids is 500 µm and 2 mm, respectively. b, Schematic representation of a human foetal brain in gestational week (GW) 5 with indicated morphogens influencing the differentiation of hindbrain rhombomeres (r) and their HOX gene code respectively. c, Heatmap showing relative bulk RNA expression of homeobox (HOX) genes at week 2 and 3 depicted as log2 fold change normalized to week 1. n = 3 pooled BrOs per batch. d, Boxplot representation of Spearman’s rank coefficient between different organoid batches from week 2 to 12. Box plots show the median (center line, 50th percentile), the box spans the interquartile range (25th–75th percentiles), whiskers extend to the most extreme observations within 1.5×IQR of the quartiles (defining the plotted minima and maxima), points beyond this range are not displayed. n = 3 organoids pooled per batch from n = 3 independent batches per timepoint. e, PCA of organoids at different timepoints from week 1 to 12 (grey scale) and derived from hESCs (circles) or iPSCs (square). n = 3 organoids pooled per batch from n = 3 independent batches for weeks 2-12; n = 3 organoids pooled from n = 2 independent batches for week 1 and n = 3 organoids pooled from n = 1 batch for iPSC-derived.
