Fig. 2: Identification of an antigen archiving gene signature.

A Ag-score is shown for day 14 Ag-high and -low cells identified for LEC subsets with the highest Ag-scores. B The fraction of cells predicted to be Ag-competent is shown for each LEC subset 14, 21, and 42 days post vaccination. Cells shown were not used for training models. C Ag-high module score is shown for Ag-low, Ag-high, and predicted Ag-competent LECs. Cells shown were not used for training models. The Spearman correlation between the ordered antigen classes and Ag-high module scores is shown for each timepoint. One-sided p-values testing for an increase in module score were calculated and adjusted using Benjamini-Hochberg correction. The center line, box limits, whiskers, and points represent the median, interquartile range (IQR), the range within 1.5×IQR from the box limits, and points outside this range (outliers), respectively. The number of cell plotted is shown below each boxplot. D UMAP projections show cLEC Ag-high module scores for each timepoint (top) and Ag-high and Ag-low cLECs (bottom). E The expression of select genes from the Ag-high (top four) and Ag-low (bottom four) gene modules is shown for cLECs. Triangles indicate the gene is differentially expressed (p-value < 0.05) when compared to Ag-low cells. P-values were calculated using a one-sided Wilcoxon rank sum test with Benjamini-Hochberg correction. Points indicate the median and grey bars show the interquartile range.