Validation of RUNX1, CTCF, and Med12 depletion and identification of RUNX1-regulated genes in LP and Phase 1 cells. (A) sgRNAs against Cbfb, Ctcf, or Med12 were introduced into Cas9-LPs. 3 days after sgRNA transduction, nuclear lysates from retrovirus-infected hNGFR⁺ cells were subjected to immunoblotting for Cbfβ, CTCF, and Med12 antibodies, while cytoplasmic lysates were subjected to immunoblotting with anti-tubulin-α mAb. (B) Volcano plots showing changes of transcriptome profiles between control and Cbfb-deficient LP (left) and Phase 1 cells (right). (C) Heatmap showing changes in the expression of RUNX-dependent and RUNX-repressed genes in LP and Phase 1 following Cbfb deletion. (D) Dot plot showing expression changes of RUNX-regulated DEGs (Fig. 3 B) in LP and Phase 1 cells following the disruption of Cbfb. (E) Venn diagrams showing the number of RUNX-dependent genes in LP and RUNX-repressed genes in Phase 1 (Fig. 3 B). Names of the three overlapping genes are shown. (F) Venn diagrams showing the number of RUNX-repressed genes in LP and RUNX-dependent genes in Phase 1 (Fig. 3 B, yellow areas). Names of the five overlapping genes are shown. Two independent experiments were performed with similar results (A). Data are presented as the average of three biological replicates (B–F). Source data are available for this figure: SourceData FS3.