CD4
Data were analyzed using the FlowSOM clustering method. First, we performed a highly detailed analysis of panel 1 at the single cell level which resulted in the identification of 346 phenotypically distinct cell clusters. For each cluster we determined the major lineage (B cells, myeloid cells, CD4Major immune lineages. As a consequence of the alemtuzumab-induced lymphodepletion, B cells and T cells were still repopulating at week 24 and did not reach baseline levels at week 52, reflected in the data by a rising number of B cells and T cells between week 24 and week 52 in both groups. There was no difference in absolute cell numbers between the control and the MSC group for B cells, myeloid cells, NK/ILCs, CD3Next, the contribution of each lineage as a percentage of the total CD45 population at each of the timepoints was assessed (Investigating the 346 phenotypically distinct cell clusters individually, 33 (of which 32 assigneable to a lineage) showed a statistically significant difference in absolute cell numbers between the control and the MSC-treated group. The 32 lineage defined clusters will be further discussed below (