Extended Data Fig. 3: Spatial analysis of T-bet⁺CXCR3⁺ B cells and activated T cells.

a, ChipCytometry of DNA (Helix-NP), CD39, CD45, CD11c and Ki67 on splenic section of PBS and EBV-infected mice. Scale bar=500μm. b, Frequency of T-bet⁺CXCR3⁺ of total B cells in spleen of PBS and EBV-infected mice (PBS n = 1, EBV n = 1). c, Frequency of EBNA2⁺ among T-bet⁺CXCR3⁺ and non-T-bet⁺CXCR3⁺ (other) B cells in spleen of EBV infected mice (PBS n = 1, EBV n = 1). d, Cell type enrichment per calculated tissue neighbourhood using HLA-DR as activation marker and e, frequency of respective tissue neighbourhoods (N-1 to N-5) in PBS and EBV-infected spleens (PBS n = 1, EBV n = 1). f-g, Frequency of activated CD4⁺ and CD8⁺ T cells (HLA-DR⁺) in the immediate microenvironment (ME; 100μm) of T-bet⁺CXCR3⁺ B cells in PBS and EBV-infected spleens (PBS n = 6, EBV n = 92 microenvironments of 1 experiment). P-values were calculated using two-sided MWU test (p-values = 0.00062 & 0.000045 respectively). h-i, Frequency of proliferative CD4⁺ and CD8⁺ T cells (Ki67⁺) in the immediate microenvironment (100μm) of T-bet⁺CXCR3⁺ B cells in PBS and EBV-infected (PBS n = 6, EBV n = 92 microenvironments of 1 experiment). P-values were calculated using two-sided MWU test (p-values = 0.0001 & 0.00014 respectively). Box plots define the medium value (centre), the interquartile range (25th and 75th percentiles) as the boundaries of the box and whiskers which extend to 1.5 times the 25th and 75th percentiles. Outliers outside the boundaries of the whiskers are displayed as individual points. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. j, Cell type enrichment per calculated tissue neighbourhood using Ki67 as a T cell proliferation marker and k, frequency of respective tissue neighbourhoods (N*-1 to N*-6) in PBS and EBV-infected spleens. l, 3D multiplex imaging by light sheet microscopy of cleared brains of two EBV-infected mice (EBV n = 3, PBS n = 1) stained for human CD3 (magenta), human CD45 (cyan) and mouse CD31 (yellow).