Supplementary Figure 1: Cell isolation and library quality checks.

(a), Flow cytometry of homogenized C57BL/6 Pep^3b mouse spleen stained with antibodies against TCRβ, CD4, CD8, CD62L, CD44. CD4⁺ T cells were isolated as TCRβ⁺ CD4⁺ CD8⁻ CD62L⁺ CD44⁻. (b), Flow cytometry of homogenized C57BL/6 Pep^3b mouse spleen stained with antibodies against TCRβ, CD19, B220, IgM, IgD. B cells were isolated as TCRβ^- CD19⁺ B220⁺ IgM⁺ IgD⁺. (c), Flow cytometry of homogenized C57BL/6 Pep^3b mouse bone marrow stained with antibodies against TCRβ, CD19, B220, Ly6C, Ly6G. Granulocytes were isolated as TCRβ^- CD19⁻ Ly6C^int Ly6G⁺. (d), Representative MA plots comparing bin pair counts between CD4⁺ T cell, B cell and granulocytes in situ Hi-C libraries, before and after normalization using a loess-based approach with the normOffsets function of the diffHic package. Y-axis shows log₂ fold change in interaction intensity while the x-axis shows average log₂ intensity. (e), Representative histogram of distribution of fragment lengths in in situ Hi-C libraries. Data derived from one of two independent experiments with similar results. (f), Representative plot of strand orientation of fragments in in situ Hi-C libraries with respect to the log-insert size (that is distance between paired reads on the same chromosome). Data derived from one of two independent experiments with similar results. (g), Percentage of DNA loop anchor bin pairs overlapped by CTCF binding sites in CD4⁺ T cells, B cells and granulocytes (Supplementary Table 18). Data derived from pool of two independent experiments. (h), Flow cytometry of homogenized cKit-enriched C57BL/6 Pep^3b mouse bone marrow stained with antibodies against cKit and Sca-1. LSK cells were isolated as cKit⁺ Sca-1⁺. (i), Multi-dimensional scaling plot showing the relationship between the interaction profiles of CD4⁺ T cells, B cells, granulocytes, LSK cells and MEFs. Distances on the plot represent leading log₂-fold-changes in interaction intensity. (j), Using the change-point detection algorithm in TADbit, we determined the number and (k), size of TADs in CD4⁺ T cells, B cells, granulocytes, LSK cells and MEFs. Data derived from pool of two independent experiments. Box plot shows median and 5^th and 95^th percentiles. (l), In situ Hi-C contact matrices of CD4⁺ T cells and B cells were overlaid with H3K27 acetylation ChIP-seq and p300 ChIP-seq (Supplementary Table 18) from each cell type. The boundaries of statistically significant DIs (FDR < 0.05) determined the coordinates shown. Color scale indicates number of reads per bin pair