Time courses of genes of interest (DEG_interest; see Table 4
b) in synovial fibroblasts from RA patients (blue and purple) or OA (red and green) stimulated with TNF-α (red and blue) or TGF-β1 (green and purple). There were only marginal differences for the gene expression values with or without BC (see also Additional file 6: Table S1). As expected, there was a clearly different regulation of the expression of 6 of 8 genes (BGN, COL1A1, COL27A1, COL5A2, COL1A2 and COL3A1; for definition of the abbreviations see Table 4) following stimulation of with either TNF-α or TGF-β1; this differential regulation was common for SFB from RA and OA patients (see Additional file 6: Table S1). However, 2 of 8 genes (COL11A1 and TINAGL) were regulated in a similar fashion by TNF-α and TGF-β1 in both RA and OA patients. Strikingly, significant differences between RA and OA patients were observed for all genes of interest already at the time point 0 hours (see Additional file 8: Table S4a). These differences were unaffected by stimulation with either TNF-α or TGF-β1.