Trancriptome analysis of XMP and MEP populations in Runx1-deficient mice. (A) Sorting strategy for analysis of bipotent MPs in Runx1^+/+ and Runx1^Δ/Δ mice. Shown are cells that have been gated for Lin⁻Sca1⁻Kit⁺CD41⁻CD105⁻. (B) Principle-component analysis was performed using DESeq2⁸²  and demonstrates the relatedness of the transcriptomes of the indicated populations. (C) Venn diagram of stringently filtered (at least threefold deregulated, false discovery rate [FDR] P ≤ .05, base mean > 100) genes whose expression is either up or down in Δ/Δ vs +/+ GMPs or MEPs. Bold numbers refer to the number of shared genes that are deregulated in GMPs and MEPs. (D) Venn diagram of stringently filtered (at least threefold deregulated, P ≤ .05) genes whose expression is either up or down in Δ/Δ XMPs vs +/+ MEPs or Δ/Δ MEPs. Bold numbers refer to the number of shared genes that are deregulated in XMP in both comparisons. (E) Bar graph showing the relative gene expression (log2) of the shared genes that are either downregulated (left) or upregulated (right) in XMPs as compared with MEPs of either genotype. Each pair of bars corresponds to the gene either to the far left (downregulated) or far right (upregulated). Heat maps show the relative expression levels of these genes in monopotent Ery or MkP progenitors or bipotent GMPS-based on normalized values in Gene Expression Commons (GEXC).⁸³  Genes not annotated in GEXC or showing spurious expression levels are not shown. (F) Relative expression levels determined from reads per kilobase of transcripts per million mapped reads (RPKM) values of genes encoding key Ery or Meg TFs are shown. Expression levels in WT MEP (+/+) were set as 1. Shown are the mean values of 2 independent experiments. Error bars, ±SD. Original P values for the comparison relative to +/+ MEP values are indicated as *P < .05, **P < .0, and ***P < .001, the latter of which have FDR P values ≤ .05. A list of all TF genes used for this analysis and gene expression levels is found in supplemental Table 2.