Figure 1
The 3D-spheroid culture of human UC-MSCs caused significant changes in gene expression. (a) Representative images of 2D- and 3D-cultured UC-MSCs under the phase-contrast microscope. (b) The difference of gene expression between 2D and 3DUC-MSCs was analyzed by RNA-sequencing; altogether 831 genes (blue) were significantly upregulated and 788 genes (yellow) were significantly downregulated in 3D UC-MSCs compared with 2D UC-MSCs (probability >80% and |log2(fold of gene expression change)|≥1). (c) The representative global view of gene expression changes between 2D UC-MSCs (n = 3, samples named 2D-1, 2D-2, 2D-3) and 3D UC-MSCs (n = 3, samples named 3D-1, 3D-2 and 3D-3) by hierarchical clustering analysis. The clusters in black denote no significant difference between 2D and 3D UC-MSCs, while the clusters in red or green denote transcripts which are more or less abundant compared to 2D UC-MSCs. The intensity of the colors is proportional to a log2 ratio of the fold of gene changes. (d) The gene ontology analysis showed the list of bioprocess terms most strongly enriched with the differentially regulated genes between 3D and 2D UC-MSCs. Each bar is proportional to the number of genes enriched in the bioprocess. Abbreviations: UC-MSCs, umbilical cord-derived mesenchymal stem cells.
