Cultured BM MSCs. (A) Phenotype of P1 cells: positive markers detected using PE-conjugated mAbs. Cells were collected at the end of passage 1 (P1, day 36), after trypsinization of confluent layers. Cells were incubated with PE-conjugated mAbs added at saturating concentration, as indicated in Document S1. (B) Phenotype of P1 cells: positive markers detected using purified unconjugated mAbs. For indirect staining, cells were incubated with the primary mouse antihuman mAbs, then with biotinylated goat anti–mouse Ig Ab, and finally with R-phycoerythrin (RPE)-conjugated streptavidin, as indicated in Document S1. (C) Hierarchical clustering. Hierarchical clustering was performed using a panel of 147 CD transcripts (genes identified as “absent” by GCOS 1.2 in all samples were excluded), on 6 independent samples of P1 MSCs, 3 samples each of CD45⁺ (CD45), CD11b⁺ (CD11b), and CD235a⁺ (GlyA) hematopoietic cells, 3 samples of periosteal cells (POC), and 4 samples of synovial fibroblasts (SFb). Clusters: i: lymphoid cluster including CD2, CD3E, CD3Z, CD8A, CD117, CD122, CD132, CD160, and CD197; ii: erythroid cluster including CD234, CD235a, CD240, CD241, and CD338; iiic: MSC cluster including CD49b, CD51, CD90, CD73, CD105, CD130, CD140a, CD140b, CD146, CD151, CD202b, CD266, CD295, CD325, and CD332; iv: SFb cluster including CD9, CD34, CD42b, CD62P, CD66d, and CD227. (D) Principal components analysis. Analysis was carried out using the same CD transcripts and on the same samples as for hierarchical clustering. Each plotted data point represents a single profile. (E) Specific CD transcripts. Among the 113 transcripts (given in Table S5) specifically expressed in cultured MSCs, 20 are CD membrane antigens. The line plot indicates the mean of signal intensities for the 6 MSC samples [S(MSC)] and the 3 samples each of CD45⁺ [S (45)], CD11b⁺ [S(11b)], and CD235a⁺ [S (235)] cells.