Fig. 2.

Runx1 and Runx3 interact with shared genomic sites that shift at different developmental stages. (A) Progenitor cells from normal bone marrow (BM) were cultured with OP9-Dll1 stromal cells for 5 d (Phase1) or for 10 d (Phase2); then, pro-T cells in Phase1 (cKit^high CD25^low) or Phase2 (cKit^low CD25⁺) were fluorescence-activated cell-sorted for chromatin immunoprecipitation with sequencing (ChIP-seq) as described in Materials and Methods. Experiment schematic and gating strategy are shown. (B) Tag count distributions for Runx1 and Runx3 in Phase1 and Phase2 stages are represented by peak-centered heat map. P1: Phase1; P2: Phase2; R1: Runx1; R3, Runx3. (C–E) Area-proportional Venn diagrams illustrate the peak overlaps of Runx1 and Runx3 ChIP-seq peaks in Phase1 and Phase2, with numbers of peaks in each category. Scatterplots compare log₂ normalized tag counts per 10 million tags for peaks in indicated categories with Pearson correlation r. (C) Promoter region peaks (TSS: transcription start site); (D) nonpromoter region peak comparison for Runx1 and Runx3; and (E) nonpromoter region comparison for Phase1 and Phase2. Data are based on ChIP-seq peaks scored as reproducible in two replicate samples (B–E).