Leukemic animals were generated as described for Figure 1. Bone marrow was harvested from 4 independent groups of mice (n = 5 per group) and purified based on expression of BCR-ABL and NUP98-HOXA9 using GFP and YFP markers, respectively. Normal and leukemic cells were further purified based on expression of lineage markers and the stem cell antigen Sca-1. As shown in the left panel, three distinct populations were isolated: lineage positive cells (population A), lineage negative progenitors (population B), and LSC-enriched, Lin−/Sca+ (population C). RNA was isolated from each purified population and analyzed using a custom Taqman Low Density Array (TLDA) designed to interrogate the CRGs. The right panel shows a heatmap of relative expression of the CRGs in mature, progenitor, and LSC-enriched leukemia cells compared to their respective normal counterparts (Green = down-regulated, Red = up-regulated).