Figure S4.
ChIP-seq analysis of RUNX1, CTCF, Med12, and Notch1-IC binding in LP and Phase 1 cells. (A) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around LP-specific RUNX1-binding regions are shown as peak-centered heatmaps. Each lane represents the merged tag directories from two biological replicates. (B) Representative ChIP-seq tracks for RUNX1 and CTCF in LP and Phase 1 around the Lck, Thy1, and Zap70 loci. CTCF-binding sites co-occupied with LP-specific RUNX1 peaks are labeled with blue rectangles. Data are representative of two independent experiments. (C) Heatmap showing changes in the expression of Thy1, Lck, and Zap70 in LP following Cbfb deletion. Data are presented as the average of three biological replicates. (D) Top three enriched sequence motifs among the 5,849 LP-specific, the 14,961 Phase 1–specific, and 24,171 shared reproducible Med12 peaks between LP and Phase 1 are shown (Fig. 5 B). Data are based on ChIP-seq peaks scored as reproducible in two replicate samples. (E) Venn diagrams show the number of shared CTCF ChIP peaks overlapping with LP-specific (upper) or Phase 1–specific (lower) Med12 and RUNX1 peaks. (F) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around Phase 1–specific RUNX1-binding regions are shown as peak-centered heatmaps. Each lane represents the merged tag directories from two biological replicates. (G) ChIP-seq data for Notch1-IC in Phase 1 and Phase 2 were analyzed. Venn diagrams show the number of reproducible Notch1-IC ChIP peaks in Phase 1 and Phase 2 cells. The top three enriched sequence motifs among the 298 reproducible Phase 1 Notch1-IC peaks (upper panel) and 709 reproducible Phase 2 Notch1-IC peaks (lower panel) are shown. (H) Venn diagrams showing the number of reproducible RUNX1 ChIP peaks in LP and Phase 1 cells, along with Notch1-IC ChIP peaks in Notch-stimulated pro-T cells (Phase 1 + Phase 2, n = 845). (I) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around Notch1-IC–binding regions in Notch-stimulated pro-T cells are shown as a peak-centered heatmap. Each lane represents the merged tag directories from two biological replicates.

ChIP-seq analysis of RUNX1, CTCF, Med12, and Notch1-IC binding in LP and Phase 1 cells. (A) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around LP-specific RUNX1-binding regions are shown as peak-centered heatmaps. Each lane represents the merged tag directories from two biological replicates. (B) Representative ChIP-seq tracks for RUNX1 and CTCF in LP and Phase 1 around the Lck, Thy1, and Zap70 loci. CTCF-binding sites co-occupied with LP-specific RUNX1 peaks are labeled with blue rectangles. Data are representative of two independent experiments. (C) Heatmap showing changes in the expression of Thy1, Lck, and Zap70 in LP following Cbfb deletion. Data are presented as the average of three biological replicates. (D) Top three enriched sequence motifs among the 5,849 LP-specific, the 14,961 Phase 1–specific, and 24,171 shared reproducible Med12 peaks between LP and Phase 1 are shown (Fig. 5 B). Data are based on ChIP-seq peaks scored as reproducible in two replicate samples. (E) Venn diagrams show the number of shared CTCF ChIP peaks overlapping with LP-specific (upper) or Phase 1–specific (lower) Med12 and RUNX1 peaks. (F) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around Phase 1–specific RUNX1-binding regions are shown as peak-centered heatmaps. Each lane represents the merged tag directories from two biological replicates. (G) ChIP-seq data for Notch1-IC in Phase 1 and Phase 2 were analyzed. Venn diagrams show the number of reproducible Notch1-IC ChIP peaks in Phase 1 and Phase 2 cells. The top three enriched sequence motifs among the 298 reproducible Phase 1 Notch1-IC peaks (upper panel) and 709 reproducible Phase 2 Notch1-IC peaks (lower panel) are shown. (H) Venn diagrams showing the number of reproducible RUNX1 ChIP peaks in LP and Phase 1 cells, along with Notch1-IC ChIP peaks in Notch-stimulated pro-T cells (Phase 1 + Phase 2, n = 845). (I) Tag count distributions for RUNX1, CTCF, Med12, and Notch1-IC ChIP peaks around Notch1-IC–binding regions in Notch-stimulated pro-T cells are shown as a peak-centered heatmap. Each lane represents the merged tag directories from two biological replicates.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal