Supplementary Figure 2: B cell–stage isolation and compartment examination.

Flow cytometry of C57BL/6 Pep^3b pro-B cell culture stained with antibodies against IgM and CD19. Pro-B cells were isolated as IgM⁻. (b), Flow cytometry of homogenized C57BL/6 Pep^3b mouse spleen stained with antibodies against TCRβ, CD19, B220, IgM, and IgD. Tr/MZ B cells were isolated as TCRβ^- CD19⁺ B220⁺ IgM⁺ IgD⁻. Follicular B cells were TCRββ^- CD19⁺ B220⁺ IgM⁺ IgD⁺ (as seen in Supplementary Fig. 1b). (c), Flow cytometry of LPS-stimulated C57BL/6 Pep^3b mouse B220⁺ splenic cell culture stained with antibodies against CD138 and CD22. Activated B cells were isolated as CD138⁻ CD22⁺. Plasmablasts were isolated as CD138⁺ CD22⁻. (d), Using the change-point detection algorithm in TADbit, we determined the number and (e), size of TADs in pro-B cells, Tr/MZ B cells, follicular B cells (as seen in Supplementary Fig. 1b), activated B cells and plasmablasts. Data derived from pool of two independent experiments. Box plot shows median and 5^th and 95^th percentiles. (f), A/B compartmental interaction plots of total chromosome 1 at six stages of B cell differentiation. 50kB resolution shown