Fig. 5: scMultiome-seq delineates GFI1-mediated epigenetic and transcriptional regulation in virus-specific CD8⁺ T cells following infection with LCMV^c13.

a, UMAP showing unsupervised clustering of 7,629 WT and 5,805 GFI1^ΔCD8 CD8⁺ T cells isolated at D7 post infection with LCMV^c13 from the spleen of C57BL/6 mice transferred i.v. with congenically labeled WT or GFI1^ΔCD8 CD8⁺ T_N cells 24 h before infection, analyzed using scMultiome-seq (scRNA-seq + scATAC-seq Seurat-integrated data). b, UMAP showing WT and GFI1^ΔCD8 CD8⁺ P14 T cell distribution in integrated data clusters as in a. c, Percentage of WT and GFI1^ΔCD8 CD8⁺ P14 T cells in each cluster as in a. d, UMAP showing normalized expression of Btg1, E2f2, Eomes and Tcf7 in WT and GFI1^ΔCD8 CD8⁺ P14 T cells as in a. e, Dot plot showing expression of selected genes in WT and GFI1^ΔCD8 CD8⁺ P14 T cells in clusters 1–7 as in a. Dot size indicates fraction of cells expressing gene; color represents mean expression. f, DEGs (top) and DARs (bottom) from cluster 1 as in a, using pseudobulk analysis of scRNA-seq and scATAC-seq, respectively. g, Selected top-ranking transcription-factor-linked eRegulons predicted by SCENIC+ analysis using scRNA-seq and scATAC-seq as in a. Color scale shows gene expression-based enrichment score; dot size illustrates chromatin accessibility-based enrichment score for each eRegulon and cell cluster. h, WT and GFI1^ΔCD8 CD8⁺ T cell chromatin accessibility and gene expression at Tcf7 gene locus in cluster 1 as in a. Dashed boxes highlight differentially accessible chromatin regions.