Figure 5.
HEL cells expressing RUNX1-WT/4A/4D reveal distinct gene expression patterns. (A) Heat map of 2625 most DEGs (adjusted P < .05) between the 3 transgene expressing HEL cells. (B) Gene expression patterns of DEGs. Most (∼80%) DEGs were grouped into the 2 largest clusters showing RUNX1-WT and RUNX1-4D decreasing (cluster 1, 1066 genes) or increasing (cluster 2, 1003 genes) expression over EV and RUNX1-4A. (C) Location of RUNX1 binding relative to the TSS for the 1550 DEGs with an associated RUNX1 CUT&RUN peak shared by all 3 (RUNX1-4A/WT/4D) transgenes. (D-E) Representative genes with increased (D, GP1BB) or decreased (E, KIT) expression by RUNX1-WT and RUNX1-4D compared with EV and RUNX1-4A with peaks near TSS. Top rows show 2 replicates of CUT&RUN for each transgene, and bottom rows show 2 replicates of corresponding RNA-seq data. (F) Plots showing DEGs between MkPs vs MEPs and ErPs vs MEPs from bulk RNA-seq data on y-axis and x-axis, respectively, with genes from cluster 1 (left, in red) and cluster 2 (right, in green) highlighted. For all DEGs, the P value cutoff was .05, and log2FC cutoff was 1. Genes that met the P value cutoff but not log2FC cutoff are localized to gray box. Number of genes that overlap with clusters 1 or 2 out of total number of DEGs, along with P values calculated by hypergeometric test are shown in each quadrant.

HEL cells expressing RUNX1-WT/4A/4D reveal distinct gene expression patterns. (A) Heat map of 2625 most DEGs (adjusted P < .05) between the 3 transgene expressing HEL cells. (B) Gene expression patterns of DEGs. Most (∼80%) DEGs were grouped into the 2 largest clusters showing RUNX1-WT and RUNX1-4D decreasing (cluster 1, 1066 genes) or increasing (cluster 2, 1003 genes) expression over EV and RUNX1-4A. (C) Location of RUNX1 binding relative to the TSS for the 1550 DEGs with an associated RUNX1 CUT&RUN peak shared by all 3 (RUNX1-4A/WT/4D) transgenes. (D-E) Representative genes with increased (D, GP1BB) or decreased (E, KIT) expression by RUNX1-WT and RUNX1-4D compared with EV and RUNX1-4A with peaks near TSS. Top rows show 2 replicates of CUT&RUN for each transgene, and bottom rows show 2 replicates of corresponding RNA-seq data. (F) Plots showing DEGs between MkPs vs MEPs and ErPs vs MEPs from bulk RNA-seq data on y-axis and x-axis, respectively, with genes from cluster 1 (left, in red) and cluster 2 (right, in green) highlighted. For all DEGs, the P value cutoff was .05, and log2FC cutoff was 1. Genes that met the P value cutoff but not log2FC cutoff are localized to gray box. Number of genes that overlap with clusters 1 or 2 out of total number of DEGs, along with P values calculated by hypergeometric test are shown in each quadrant.

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