HSPCs from RAG1-SCID patients have a uniform stem and progenitor phenotype at the start of the ATOs. Gated populations within the CD34⁺-enriched HSPCs are defined as follows, in addition to positive gating for CD45: B cells, CD19⁺CD123^–; myeloid, CD123⁺CD19^–; CMP (common myeloid progenitor), CD34⁺CD38⁺; LMPP (lymphomyeloid primed progenitors), CD34⁺CD38^–CD90^–CD45RA⁺; MPP (multipotent progenitor), CD34⁺CD38^–CD90^–CD45RA^–. Short-term HSC: CD34⁺CD38^–CD90⁺CD45RA^–. Long-term HSC: CD34⁺CD38^–CD90⁺CD45RA^–CD201⁺CD49f⁺. Controls from UCB and mPB; patients: p1, p2, and p3. (A) Flow cytometry plots of gated populations, as indicated. (B) Relative distribution of the different HSPC populations. (C) UMAP based on 17 markers as shown in panel D with the exception of CD10 (supplemental Table 1), including 3 patient and 2 control samples. A total of 643 743 CD45⁺ cells are included. The different progenitor populations (as gated in panel A) are overlaid (top row, left) and separately (others, top row), as well as the overlaid expression of selected markers (bottom row). Red, high expression; blue, low/no expression. (D) Heat map of gated CD34⁺ HSPCs based on the median expression of all markers. The small B-cell and myeloid cell populations from 2C were only present in patients’ HSPCs and omitted from the heat map.