Notch1 and Tcf1 epigenetically establish T-lineage specification in early BM progenitors. (A) Induced CD45.2⁺ BM cells from Controls (black, n = 3), Tcf7^Δ/Δ (light blue, n = 3), N1IC (red, n = 3), or N1IC Tcf7^Δ/Δ (blue, n = 3) mice were FACS purified for lineage^-, cKit⁺ (CD117), and Sca1⁺ BM progenitors (LSK) for ATAC-seq analysis. Characteristic flow cytometric plots are shown. (B) Heatmap depicting all regulated genomic loci in comparison N1IC vs Controls and then used as a reference and compared with N1IC Tcf7^Δ/Δ (FDR < 0.01) for ATAC-seq called and centered peaks, shown for all experimental groups. Color scale for centered values is shown below the heatmap. (C) Enrichment of biological pathways from gene ontology biological process (GOBP) collection in genes with induced proximal accessibility by N1IC and Tcf7. Top 20 pathways are shown from ontologies with a fold enrichment >2 and FDR <0.05. P values were calculated with Fisher's exact test. (D) Integrative genomics viewer chromatin accessibility profiles for all experimental groups are shown at the promoter of Ptcrα and for Cd3ε. Tracks were group-scaled. Schematic representation of genetic loci is depicted below the profiles. (E-F) Footprint analysis for transcription factors binding regulated by (E) N1IC vs Controls and (F) N1IC vs N1IC Tcf7^Δ/Δ.