RNA sequencing analysis of Hhex overexpression in LSK cells. (A) RNA Seq trace showing expression of Hhex in LSK cells 2 days postinfection with control (MIG) or Hhex-expressing (MIG-Hhex) retroviruses. Units are reads per million mapped reads (RPM). (B) Waterfall plots showing RNA Seq analysis of the top 20 downregulated genes (left panel) and upregulated genes (right panel) in LSK cells 2 days postinfection with control or Hhex-expressing retroviruses (n = 3). (C-D) Inverse correlation between Hhex-overexpressing and -knockout LSK cells. Genes that are significantly upregulated (C) and downregulated (D) following Hhex deletion in LSK cells in vivo were compared in control (MIG) and Hhex-overexpressing (MIG-Hhex) LSK cells using gene set enrichment analysis. In panel C, the enrichment plot (left) demonstrates that genes upregulated in Hhex-knockout LSK cells are repressed in Hhex-overexpressing (MIG-Hhex) LSK cells, whereas the heat map (right) shows the relative expression of the top 30 genes that are both upregulated following Hhex deletion and downregulated following Hhex overexpression. In panel D, the enrichment plot (right) demonstrates that genes downregulated in Hhex-knockout LSK cells are upregulated in Hhex-overexpressing LSK cells, whereas the heat map (right) shows the relative expression of the top 30 genes that are both downregulated following Hhex deletion and upregulated following Hhex overexpression. FDR, false detection rate; NES, normalized enrichment score.