Organization of LP-specific RUNX1/CTCF repressive complex and Phase 1–specific RUNX1/Med12/p300/Notch1-IC activation complex at the Notch3 and Hes1 loci. (A) Experimental scheme for the transcriptome analysis. (B) 5 days after sgRNA introduction, hNGFR⁺CD45⁺ LP cells were sorted, and subjected to QuantSeq 3′ mRNA sequencing. The heatmap shows the expression changes of representative RUNX1- and CTCF-repressed genes among Notch-activated genes in pro-T cell stages (Romero-Wolf et al., 2020). Data represent the average of three biological replicates. (C and D) Representative ChIP-seq tracks for RUNX1, CTCF, Med12, and p300 in LP and Phase 1 cells, Notch1-IC in LP, Phase 1, and Phase 2 cells, RUNX1 in sgControl- or sgCTCF-transduced LPs, and Med12 in sgControl- or sgCbfb-transduced Phase 1 cells around the Notch3 (C) and Hes1 (D) loci are shown. CTCF-binding sites co-occupied with LP-specific RUNX1 peaks are labeled with blue rectangles, whereas Phase 1–specific RUNX1/Med12/p300/Notch-IC–binding sites are marked with red rectangles. Data are representative of two independent experiments.