Fig. 6: Single cell RNA-sequencing of Tnmd^−/− ScxGFP⁺ and WT ScxGFP⁺ cells isolated from non-injured Achilles tendons.

A Volcano plot shows –Log₁₀FDR i.e. adjusted p-value and Log₂Fc expression values of all genes, each dot represents a gene. Significantly differentially expressed genes (DEGs) (–Log₁₀FDR < 0.05 and |Log₂ Fc | > 1) are highlighted in color other than gray. Vertical lines present the Log₂Fc threshold equaling 1 or −1; genes outside these lines are DEGs with at least 2-Fc. The horizontal lines show –Log₁₀FDR corresponding to FDR thresholds of 0.05, 0.001 and 0.0001 from the bottom respectively. Red, purple and blue dots represent the significant DEGs with 2-Fc and –Log₁₀FDR < 0.0001, –Log₁₀FDR < 0.001 and –Log₁₀FDR < 0.05 respectively. Gray dots are neither significant nor have expression above 2-Fc. B Heat map depicting the Log₂CPM expression value of selected top 100 significant DEGs. Top 100 genes with lowest q-value are depicted. Genes are colored according to their Log₂CPM expression values. Clustering on the top is based on cell type and degradation level. C–E GO enrichment analysis of the significantly DEGs; results are depicted in dot plot format where top 10 enriched ontology terms are listed on y-axis and the percentage of hits (number of DEGs/number of background genes associated to each term) are indicated on x-axis. Dots size represents the count of DEGs associated with each term, whilst the color shows the enrichment p-value. Top enriched terms from C Biological Process, D Molecular Function and E Cellular Component. F KEGG signaling pathway analysis of the significant DEGs in dot plot format; y-axis shows top 15 enriched pathways; x-axis indicates gene ratio (number of DEGs/number of background genes associated to each term). Dots size is based on the number of DEGs that were associated with each term, whilst the color shows the p-value of enrichment.