When we queried each cluster for enrichment of either LSC or HSC-like gene signatures the analysis clearly demonstrated that the primitive cells from CML samples could be divided based on the presence of BCR:ABL1, where CML cluster 3 displayed an evident enrichment of BCR::ABL1+ LSC specific signatures as compared to CML cluster 2 consisting of BCR::ABL1- non-leukemic stem cells (Figure 4—figure supplement 1D–E). Here, ABL1 is linked to chronic myelogenous leukemia, BCR-ABL1 positive.