Fig. 2

Transcriptome analysis. A PCA plot of single cells based on expression levels (genes with TPM ≥ 10 in at least one cell). T1, at the time of 3D culturing; T2 and T3, after the first and second transplantations, respectively. n = 42, 42, and 51 cells for T1, T2, and T3, respectively. B Boxplots of Euclidean distance from the centroid in the PCA space (using full dimensions). **: P < 0.01 (two-sided Wilcoxon rank sum test). C Heatmap of gene expression levels (in TPM). The rows represent single cells or bulk-cell samples (in the bottom), and the columns represent highly variable genes and several types of marker genes. The cell and gene groups were determined as shown in Additional file 1: Figure S4. The red, blue, and green codes in the rows correspond to T1, T2, and T3. “Diff.” and “Prol./cell-cyc.” represents differentiation and proliferation/cell cycle. “APC_ctrl” indicates control samples that were cultured in our 3D culture system and derived from normal cells without APC knockdown. D PCA plot of cells grouped based on expression levels of highly variable genes