This report explores the effect of Hif-1alpha deletion, using a conditional mouse model, together with standard chemotherapy regimen to evaluate leukemia stem cell (LSC) targeting in a murine model of MLL-AF9 driven acute myeloid leukemia (AML). This study reveals that Hif-1alpha-deleted leukemias displayed a faster disease progression after chemotherapy. Overall design: Single cell RNA-seq data were generated on the 10X emulsion platform (10X Genomics, Pleasanton, CA) according to the manufactures instructions. The single-cell RNAseq from the Chromium platform was processed using CellRanger v1.3 using default settings, and subsequent normalization, QC, filtering, and differential gene expression analysis was performed in R using Seurat v1.4 (http://www.satijalab.org/seurat). Dimension reduction was performed using DDRTree over three components.