Deletion of Hoxa cluster genes in adult mice and transcriptome analysis of Hoxa^−/− HSCs. (A) Bar graphs depicting absolute numbers of CD150⁺/CD48⁻/CD244⁻/LKS HSCs and CD150⁺/CD48⁻/CD244⁺/LKS MPPs in BM of Hoxa^−/− and control mice (n = 4). BM cells isolated from femur and tibia 4 weeks after pIpC injection. (B) Polymerase chain reaction analysis showing the deletion of the Hoxa cluster in purified LKS cells at 4 weeks following the last pIpC injection (n = 5). (C) Engraftment of Hoxa^−/− (n = 14) and control (n = 15) cells in the PB, BM, spleen, and thymus of recipient mice at ∼24 weeks after transplantation. Each dot represents a CD45.1 recipient mouse transplanted with 10⁶ congenic CD45.2 BM cells. (D) Proportions of B (B220⁺), myeloid (Mac1⁺), T (CD3⁺), and erythroid (Ter119⁺) cells in PB of reconstituted mice shown in (C). (E) Scatterplot showing transcriptome analysis of genes that were up- (above axis) or downregulated (below axis) in Hoxa^−/− vs WT control CD150⁺/CD48⁻/LKS cells sorted 1 month after the last pIpC injection. Values are expressed as average (log10 [(average RPKM)*1000 + 1]). Cut-off limit for showing gene identify was set at 3, representing a RPKM value of ∼0.1. Highlighted genes show 10-fold differences between the 2 groups. (F-G) Comparative expression of Hoxa (F) and Hoxb (G) genes in pairs of Hoxa^−/− and control HSC samples (n = 3). *P < .05; **P < .01; ***P < .001. Cre, causes recombination; CT, cycle time; HPRT, hypoxanthine-guanine phosphoribosyltransferase; MPP, multipotent progenitors; RQ, relative quantification; Spl, spleen; Thy, thymus.