RNAseq analysis after IKAROS depletion reveals a stem cell–like gene expression pattern and upregulation of AML stem cell–associated genes. (A) Gene set enrichment analysis shows gene expression changes in signatures associated with hematopoietic stem cells (HSC), AML leukemia stem cells (AML SC CE HSC LSC), and the IL7/JAK/STAT pathways after IKZF1 knockout. Data shown are a representative example from a single pairwise gene set enrichment analysis of one WT and one IKZF1 KO experiment from 3 replicates. (B) Volcano plot showing the most statistically significantly upregulated and downregulated genes (IKZF1 KO vs WT). Parenthetical numerals next to gene identifiers indicate multiple isoforms of one gene. Genes highlighted in blue are included in confirmatory follow-up in other figures. ES, enrichment score.