Extended Data Figure 4. Enhancer priming mediates early chromatin accessibility at T_EFF loci.

a, Heatmap of Z scores of TPM-normalized RNA-seq reads across the k-means clustered (k=10) transcriptomes (less genes robustly expressed in PB_EFF cells) of ETP, DN2a, Lin⁻c-Kit^intCD25^hiCD44^hiCD4⁻CD8⁻ (DN2b), DN3, CD4⁺ T_{EFF cd3/cd40}, CD4⁺ T_pan, T_CM, CD8⁺ T_EFF, T_RM, T_H17_CNS, T_H17_gut, T_FH, T_H1 and T_H2 cells (n=2 for each). b, Heatmap of Z scores of TSS-normalized ATAC-seq fragments across the k-means clustered (k=9) T_EFF loci in ETP, DN2, DN3, T_RM, CD8⁺ T_{EFF in vitro}, CD8⁺ T_EFF, T_CM, T_H1, T_H2, T_H17_CNS, T_H17_gut, T_FH cells and B_EFF cells (n=2 each). Labeled columns highlight ATAC-seq peaks whose nearest gene represents a canonical gene reflective of a distinct T effector program. c, Representative aggregate histograms of H3K4me1³¹ (1 of n=2), H3K4me3³¹ (1 of n=2), H3K27ac³² (1 of n=2) or RNA Polymerase II³¹ (POL II) (1 of n=2) ChIP-seq or GRO-seq dyads intersecting all T_EFF loci (blue), T_EFF loci near active genes in ETP-DN3 cells (blue) and all non-T_EFF loci (green) in DN2-DN3 thymocytes. d, Representative aggregate histograms of H3K4me1³¹ (1 of n = 2), H3K4me3³¹ (1 of n = 2) ChIP-seq dyads at promoter vs. gene-distal T_EFF loci in DN2-DN3 thymocytes.