Fig. 2

scRNA-TCRseq of human cerebrospinal fluid reveals clonally expanded CD8⁺ T cells. a Seurat dimensionality reduction and clustering of 22 CSF samples that passed quality control displayed on tSNE (GNLY: Granulysin; DCs: Dendritic Cells). b Heatmap of cluster marker genes used to annotate clusters. c Cells with detected TCR displayed on tSNE. d CD3D expression displayed on tSNE. e Quantification of average cell type distribution based on Seurat clustering. f Clones – cells with TCR sequences shared with other cells – displayed on tSNE. Only cells with detected TCRs are included. g Clones of different sizes displayed on tSNE. Only cells with detected TCRs are included; lower right heatmap shows significant differentially expressed genes between clone size bins. h Quantification of number of T cell types per clone size. Only cells with detected TCR are included. GNLY⁺CD8⁺ T Cells and CD8⁺ T cells were combined as CD8⁺ T cells. i Quantification of % T cell types per clone size