Fig. 2: Single-cell RNA sequencing shows an increase of hybrid state in MG organoid embedded in Collagen 1 and stiff matrix.

UMAP dimensionality reduction plots with different colors representing unsupervised clustering: Integrated data using Seurat (a) and the plot of integrated data split by different conditions as indicated (b). HY stands for hybrid and Pr stands for proliferating cells. Integration of data did not bring an over-correction of the data or disappearance of certain population. Quantitative assessment of LC and BC marker gene expression in MATR (c), SOFT (d), COL1 (e), and STIFF (f) condition: Scatterplot with the x-axis representing the adjusted proportion of BC-specific marker genes and the y-axis representing the adjusted proportion of LC-specific markers. The proportion of cells which express more than 65% (0.65) of BC and LC markers is indicated as red square. g Quantification of cells in each data considered as hybrid status, indicated as red square on 2 (c–f). Slingshot pseudotime trajectory analysis: UMAP dimensionality reduction plots of integrated data for the trajectory and quantification of pseudotime as violin plot composed of trajectory 1: BC – BC Primed – LC ER+ (h), trajectory 2: BC – BC Primed – HY BC/ER- – LC ER- (i) and trajectory 3: BC – BC Primed – HY BC/ER- – LC ER- – HY ER+/ER- – LC ER+ (j). BC primed indicates BC primed LC differentiation cluster. Triangle indicates start of trajectory and square indicates termination of trajectory. Heatmaps illustrate the expression levels of genes that are differentially expressed along the trajectories in the integrated dataset, encompassing marker genes for BC, LC ER+, and LC ER-: trajectory 1 (k), trajectory 2 (l), trajectory 3 (m). Source data are provided as a Source Data file.