Fig. 1. Generation of a scRNA-seq dictionary of gene expression signatures in more than 17 immune cell types in response to each of 86 cytokines in vivo.
a, Schematic of the experimental and computational workflow. First row, data generation procedures; second row, illustration of the Immune Dictionary and its companion software IREA; third row, analyses of the Immune Dictionary. b, t-distributed stochastic neighbour embedding (t-SNE) map of all cells collected from lymph nodes after cytokine stimulation or without stimulation (PBS controls) coloured by cell-type identity. Cells were sorted to rebalance frequencies of major cell types. c, Violin plots of expression levels of well-established cytokine-responsive genes following PBS or cytokine treatment. ***False discovery rate (FDR)-adjusted P < 0.001, two-sided Wilcoxon rank-sum test. d, Quantitative representation of overall transcriptomic response levels in each cell type 4 h after cytokine stimulation compared with PBS controls. Each cell type is analysed independently and is represented by a distinct colour, following the colour codes in b and c. Colour saturation indicates the magnitude of the response. Size indicates the number of genes with significant differential expression (absolute log2(fold change (FC)) > 0.25 and FDR-adjusted P < 0.05, two-sided Wilcoxon rank-sum test) in each cytokine signature.