Extended Data Figure 1. T effector loci reflect the chromatin and transcriptional profiles of major T effector subtypes.

a, Heatmap of Z scores of TPM-normalized RNA-seq reads across the k-means clustered (k=7) transcriptomes (less genes robustly expressed in B_EFF cells) of sorted CD4⁺CD44⁺TCRβ^lo splenic T cells²¹ 18h post-injection with CD3/CD40 Abs (hereafter CD4⁺ T_{EFF cd3/cd40}), splenic CD19⁻CD8⁻TCRβ⁺CD4⁺ T cells²¹ (hereafter CD4⁺ T_pan), T_CM, CD8⁺ T_EFF, T_RM, T_H17_CNS, T_H17_gut, T_FH, T_H1, T_H2 and CD11b⁻NK-1.1⁻TCRβ⁻CD138⁺Blimp1^intMHCII^hi plasmablast cells²¹ (hereafter PB_EFF) (n=2 each). b, Distribution of genomic displacement of T effector loci (hereafter T_EFF loci) in relation to the nearest TSS (signed logarithmic scale). c, Heatmap of statistical enrichment (one-sided Fisher’s exact test) of T_EFF peaks whose nearest gene is in RNA-seq k-means cluster i (horizontal axis) within an ATAC-seq k-means cluster j (vertical axis; see Fig. 1a). d-g, Representative flow cytometry plots illustrating gating strategy for in vivo DN thymocyte FACS. h, Representative distribution (for all ATAC-seq samples) of normalized Tn5 insertions within 2 kb of transcriptional start-sites (TSS). i, Representative genome browser of ATAC-seq in ESC²⁹, HSC¹¹, MPP¹¹, CLP¹¹, ETP, DN2a, DN3, DN4, DP, CD8 SP, T_N, T_EFF cells and B_EFF cells at Gzmb (T_EFF=CD8⁺ T_{EFF in vitro}) and Ifng (T_EFF=T_H1) loci (1 of n=2 for each). Adjoined bars indicate RNA-seq-determined transcripts-per-million (TPM) in each cell type.