Supplementary Figure 4: Focused analysis of kidney T cells and NK cells.

a, The expression of selected genes across the 7 high-level T/NK cell clusters. b, The expression of selected genes across the two subclusters of cluster CT5, and in comparison to cluster CT1. c, The expression of genes associated with exhaustion, across the different T/NK cell clusters. d, A heatmap showing the separation of LN patients (orange in line above heatmap) and healthy controls (blue), based on expression data of CD8⁺ T cells sorted from blood samples, and considering a published list of exhaustion markers. Both rows and columns are clustered based on Euclidian distance. Note that out of the 10 LN patients for which blood samples were available, only 8 had sufficient numbers of blood CD8⁺ T cells to allow sequencing. e, The exhaustion score as calculated in blood CD8⁺ T cells, comparing the 8 LN patients to the 10 healthy controls. Each point represents a single patient; lines represent the median per group. **—p-value < 0.01 (two-tailed Mann-Whitney U-test). f, The exhaustion score in kidney CD8⁺ T cells, comparing LN patients to LD controls (same 8 LN patients as in (e)). Each point refers to a cell. g, The expression of selected genes across the two subclusters of cluster CT3. h, The expression of selected genes across the two subclusters of cluster CT0a.