Fig. 6

RNA-seq data of MSCs in 3D and 2D culture. (A) Volcano plot of the total RNA transcripts. 371 genes showed significant (> 2-fold change, FDR < 0.05) upregulation in their expression (red dots), while 476 genes showed significant downregulation in their expression (blue dots) in 3D culture compared to 2D culture. (B) Genes with significant alterations in their expression are illustrated in the heatmap. The cell samples clustered according to how they were cultured (2D vs. 3D) and not according to their origin. (C) Metascape analysis for top enriched clusters of differentially expressed genes. (D) Top enriched KEGG pathways based on gene expression patterns. The full list is available in the Supplementary Material 4. Red bars illustrate upregulated genes, and the blue bars are downregulated genes. (E) The ECM-Receptor interaction KEGG pathway illustrates upregulated genes (red) and downregulated (blue) genes. The boxes with both colors represent gene families with different expression patterns. (F) Gene Ontology (GO)- Cellular Compartments analysis representing the top identified categories. For representation purposes, “Cytoplasm” corresponds to the total number of genes of the ‘cytoplasm’ and ‘cytosol’ categories of the GO, “Nucleus” corresponds to the total number of genes of the ‘nucleus’ and ‘nucleoplasm’ categories of the GO, “Plasma membrane” corresponds to the total number of genes of the ‘plasma membrane,‘ ‘membrane,‘ ‘integral component of plasma membrane’ and ‘integral component of membrane’ categories of the GO, and “Extracellular region” corresponds to the total number of genes of the ‘extracellular region,‘ ‘extracellular space’ and ‘extracellular matrix’ categories of the GO. Duplicated genes were calculated only once. Red bars represent upregulated genes, and blue bars represent downregulated genes. (G) Log2 fold- change difference of MSC genes related to osteogenesis (grey bars) and adipogenesis (beige bars) in 3D culture versus 2D culture