Fig. 2

Comparison of microchip hybridizations for RNA from BS cells and BMSCs. a Significance analysis of microarray (SAM) revealed the number of probesets, which were upregulated (red circle) and downregulated (green circle) in BS cells as compared to BMSCs as well as the number of unregulated probesets (intersection). b Regulation of selected probesets from three BMSC donors and three BS cell donors. Upregulated probesets are represented by red areas, downregulated by green ones with light colors indicating stronger regulation than darker colors. c Validation of the microarray results using RT-PCR with three biological replicates for each cell source for the genes fibroblast growth factor (FGF) 9 and 18, proteoglycan 4 (PRG4), mesenchyme homeobox 2 (Meox), CD200, forkhead box P2 (FOXP2), integrin-binding sialoprotein (BSP), WNT1 inducible signaling pathway protein 3 (WISP3) and EF1α serving as normalization control. d Gene Ontology (GO) analysis of all differentially expressed probesets (3,153 altogether) identified significantly enriched “molecular function”, “cellular component” and “biological process” GO clusters. Shown are various sub-clusters identified in each major GO cluster. e RT-PCR analyses of the expression of the epithelial marker mucin 1 (MUC1) in three different donors for each cell type, with EF1α serving as normalization control. BMSCs bone-marrow derived mesenchymal stem cells BS bursa subacromialiss