Microarray analyses of CD34⁺/CD38⁻LSCs. Microarray analyses were performed on RNA from highly purified (sorted) CD34⁺/CD38⁻ AML LSCs (A) and CML LSCs (B), as described in supplemental Patients and methods. All samples were obtained at diagnosis. The heat maps show the 50 top upregulated genes (left panels, A-B) and the 50 top downregulated genes (right panels, A-B) encoding accessible surface molecules in CD34⁺/CD38⁻ cells in 3 patients with AML (patients #102, #173, and #210) and 3 patients with CML (patients #8, #11, and #21) compared with normal BM stem cells. Relative expression levels of messenger RNA (normalized to normal BM stem cells) are defined by the color score (log2 fold changes), as indicated. Patient numbers refer to the patient numbers shown in supplemental Tables 2 and 3.