Gelfoam scaffolds

For the proteomics experiments, cocultures of DPSCs with LECs and of DPSCs with BECs were seeded into Gelfoam scaffolds (Pfizer) and subjected to cyclic stretch. After 14 d of culture, constructs were digested by trypsin, analyzed by liquid chromatography–mass spectrometry on a Q-Exactive plus (Thermo), and identified by Maxquant (Mathias Mann's laboratory, Max Planck Institute) software against the human proteome—part of the Uniprot database and a decoy database (in order to determine the false discovery rate [FDR]). Quality control was performed on the proteomics data, and only proteins with 2 Razor + unique peptide and above were further analyzed, to increase the certainty of protein identification. t test was performed on the normalized intensities between the two coculture groups (DPSCs with BECs versus DPSCs with LECs). Significant differentially expressed protein levels between the two groups were defined as proteins with at least 3 ms/ms count and FDR adjusted P value below 0.05. In total, 147 proteins with statistical expression differences were detected between BECs and LECs (reference Dataset S1). A heatmap of these proteins was generated based on the Z-score of their normalized intensities (SI Appendix, Fig. S7), using ComplexHeatmap R package version 2.6.2 (37 (link)). All analyses were conducted using R version 4.0.5.