Fig. 7: scRNA-seq of lymph node cells from immunized VRC01 knock-in mice.

a Graph-based clustering and t-distributed stochastic neighbor embedding (tSNE) dimensionality reduction plots of single-cell RNA-seq of 10,226 cells from 2 control, 7679 cells from 2 CTLA-4 Ab treated and 7938 cells from 2 OX-40 Ab treated mice lymph node tissue after the completion of immunization. 13 distinct transcriptional clusters were identified on the aggregated cells. b Feature plots of the expression of individual transcripts on the tSNE plot to identify B cells (Cd79a), CD4 T cells (Cd4), CD8 T cells (Cd8a) and activated/regulatory T cells (Ctla4). c Heatmap of the top 5 upregulated genes in each of the 13 transcriptionally identified clusters. Expression of individual genes shown for 100 cells for each cluster or all cells if less than 100 cells in cluster. d tSNE plots showing cells from control mice (blue), CTLA4 Ab treated mice (red), OX40 Ab treated mice (green) and all groups together (total). e, f Venn diagram of significantly changed genes determined using a likelihood-ratio test (P < 0.05) comparing all cells (e) or only B cells (f). Selected transcripts identified that are upregulated compared to control (red font) or downregulated (green).