Figure 5.

Extracellular matrix responses to transforming growth factor-β (TGF-β) stimulation are altered in the absence of Ptpra. Wild type WT and Ptpra^−/− murine embryonic fibroblasts (MEFs) were stimulated with 2 ng/mL of TGF-β for 24 h and harvested for bulk RNA sequencing. The “ECM Organization” GO term pathway was interrogated. A: principal component analysis (PCA) shows clear clustering of transcriptomic data. A single sample (WT, TGF-β, 24 h stimulation) was excluded due to poor quality RNA. B: heatmap of differentially expressed genes (DEGs) within the “ECM Organization” GO term pathway that were significant for the interaction comparison between WT and Ptpra^−/− after stimulation with TGF-β at a false discovery rate (FDR) of 0.05. C: bar plot of the “parent” ECM Organization GO Term (GO:0030198) and its “children” ordered by P value significance on the y-axis, with x-axis showing the fraction of overlap between the GO term’s annotated genes and the significant genes in the analysis. D: scatterplot of genes within the ECM Organization GO term pathway. The x-axis shows log2-fold change for TGF-β over buffer in the WT fibroblasts, and the y-axis shows log2-fold change for TGF-β over buffer in the Ptpra^−/− cells. Genes that reached significance are shown in orange. E: a subset of genes within the ECM Organization GO term that demonstrate differential responses to TGF-β based on genotype (WT vs. Ptpra^−/−) are shown.