Extended Data Fig. 10: Matrix impacts organoid patterning and regionalization.

a-b) UMAP embedding of scRNA-seq data with cells colored by condition (a) and cell population (b). Stacked barplot shows cluster proportion per condition. Abbreviations: Non-telen. = Non telencephalic, PSCs = Pluripotent stem cells. A star indicates p < 0.05, calculated using a Fisher’s exact test between the cluster proportions of Matrigel and no-matrix or agarose conditions, corrected for multiple testing using the Benjamini-Hochberg method. For p-values see Supplementary Table 13. c) Volcano plot highlights differentially expressed genes between Matrigel and no-matrix conditions calculated using a non-parametric Wilcoxon Rank Sum test with p-value cutoff using adjusted p-value. The p-value adjustment was performed using Bonferroni correction based on the total number of genes in the dataset. Positive and negative log fold change indicates genes with higher expression in Matrigel or higher expression in no-matrix conditions, respectively. GO/KEGG terms enriched for genes differentially upregulated between Matrigel (right) and no-matrix (left) conditions are shown. Heatmaps show average gene expression of selected differentially expressed genes in different regions of the human fetal brain tissue from 5-14 post-conceptional weeks³⁵. d) Cross sections from a whole mount fluorescence in situ hybridization chain reaction (HCR) staining for selected differentially expressed genes between Matrigel and no-matrix conditions. Scale, 100 micrometers. n = 3. e) Violin plots showing the total protein expression in Matrigel and no-matrix organoids over time and calculated from the 4i experiment shown in Fig. 4 and Extended Data Figs. 8 and 9. The boxes of the violin plots show the interquartile range, the line at the center is the median and the whiskers extend to the data range excluding outliers. A star indicates p < 0.05, calculated using a Wilcoxon rank sum test (two-sided) between conditions corrected for multiple testing using the Benjamini-Hochberg method. For p-values see Supplementary Table 13. n = 5289 (Day 7), n = 11690 (Day 15), n = 16168 (Day 21).