Bulk genomic studies of tens of thousands of acute myeloid leukemia (AML) cells mixed together have cataloged the changes in gene expression and mutations present in at least 10-20% of cells. The discoveries from these studies have implicated a number of new genes in AML formation, progression, and persistence, resulting in further subclassification of the disease. Still, these discoveries have thus far not been translated into improved outcomes for patients. This is in large part due to the heterogeneity of cell types and genomic changes within the cells that are present within a sample. The development of technologies to sequence genomes, quantify transcriptomes and identify surface proteomes of single cells has afforded a new opportunity to dissect and better understand the biology of these distinct cell types. In this study, we perform single-cell RNA sequencing and CITE-seq of 30 AML samples. Using cell types identified from single-cell RNA-sequencing with CITE-seq, cells are sorted based on expression of surface markers unique to phenotypic AML subpopulations. This is followed by whole genome amplification using our newly invented primary template-directed amplification (PTA) to perform accurate variant calling of the 1.2 Mb of the genome most commonly mutated in AML samples, as well as low-pass whole genome sequencing for single cell copy number variation profiling. Data from these studies will be used to identify distinct cell types present in AML samples including cells that appear to be of non-myeloid origin. This data will enable the exploration of transcriptomic changes present in distinct AML subpopulations. We anticipate the new insights afforded by this high-resolution resource will provide a deeper understanding of AML that could uncover new treatment approaches for this deadly pediatric cancer.