Fig. 2

Transcriptional characterization of the collagen sphere. A Principal component analysis of RNA-seq data from MG-ENR, COL-ENRWN, and dFEnS based on the 12,137 variably expressed genes, of which adjust p value<0.1, is shown. B Venn diagram depicts the significant overlap of differentially expressed genes (DEGs) (padj<0. 1, FC≥2) between COL-ENRWN and dFEnS (N=2). Up in COL (red and yellow) indicates the numbers of genes upregulated in COL-ENRWN compared to MG-ENR (1880 genes); Up in dFEnS (green and yellow) represents the numbers of genes upregulated in dFEnS compared to MG-ENR (1769 genes). Total of 1262 genes are overlapped between these 2 gene sets (yellow). The p value of statistical significance is indicated. C Top 20 GO-TERM (BP direct) of upregulated gene set in COL-ENRWN compared to MG-ENR is shown. D Top 20 KEGG pathway enriched in upregulated gene set in COL-ENRWN compared to MG-ENR is shown. E A volcano plot of DEGs (padj<0. 1, FC≥2) between MG-ENR and COL-ENRWN with DEGs indicated. Each plot indicates the gene with the average log 2-fold change (x-axis) and -log10(p value) (y-axis) of duplicate samples of each condition. F The RNA sequencing tracks of Wwtr1, Fn1, Ctgf, Il33, and Tacstd2 in MG-ENR (blue), COL-ENRWN (red), and dFEnS (green) are shown