This PDF file includes:

• Supplementary Materials and Methods
  
• fig. S1. Experimental schemes for the different transplantation settings described in the paper, using both mouse and human HSPCs.
  
• fig. S2. Analysis of the engraftment of murine HSPC subpopulations in BU_TX or irradiated mice.
  
• fig. S3. FACS plots of cell populations sorted for gene expression analysis.
  
• fig. S4. Evaluation of hCD34⁺ cell engraftment in BM and brain of transplanted NSG mice.
  
• table S1. ANOVA P values with Tukey’s post hoc test of contrasts between cells in Fig. 4B.
  
• table S4. Moderated t test (limma) after FDR (46) adjustment for the different contrast of interest.
  
• Legends for tables S2 and S3A to S3D

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Other Supplementary Material for this manuscript includes the following:

• table S2(Microsoft Excel format). Differential expression of RNA-seq profiles ofμ and TAμ cell populations.
  
• table S3A (Microsoft Excel format). Genes up-regulated in μCT versus μBU_TX as per Fig. 5A.
  
• table S3B (Microsoft Excel format). Genes down-regulated in μCT versusμBU_TX as per Fig. 5B.
  
• table S3C (Microsoft Excel format). Genes up-regulated in μCT versus TAμBU_TX as per Fig. 5C.
  
• table S3D (Microsoft Excel format). Genes down-regulated in μCT versus TAμBU_TX as per Fig. 5D.