Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node

A two-sided Wilcoxon rank-sum test was used to compare relative ova signal for each cell type. Relative ova signal was calculated by dividing antigen counts for each cell by the median antigen counts for T and B cells. The Bonferroni method was used to correct for multiple comparisons. The number of cells in each group (n cells), fraction of the total cells for the sample (frac cells), median relative ova signal, test statistic (statistic), estimation of the median difference (estimate), and confidence interval (conf.low, conf.high) are included.

Ova-low and ova-high cells were independently identified for each cell type shown in Figure 3 using a Gaussian mixture model implemented with the R package mixtools. Differentially expressed genes were identified using a Wilcoxon rank-sum test performed using the R package presto (wilcoxauc). The Benjamini–Hochberg method was used to correct for multiple comparisons. Genes were filtered to only include those with an adjusted p-value<0.05, log fold-change >0.25, area under the receiver operator curve (AUC) >0.5, and with at least 50% of ova-high cells expressing the gene. The average expression, log fold-change, test statistic (statistic), AUC, percentage of ova-high cells that express the gene (pct_in), and percentage of ova-low cells that express the gene (pct_out) are included.

Ova-low and ova-high cells were identified independently for DCs, FRCs, and LECs using a Gaussian mixture model implemented with the R package mixtools. Differentially expressed genes were identified as described for Figure 4—source data 1.