Comparison of steady-state spleen DC subsets.

(A) Steady-state splenic DCs were magnetic bead-enriched for CD19⁻B220⁻CD3⁻Gr-1⁻Ter119⁻CD11c⁺ cells. MHCII⁺CD11c⁺ cells (circled) were then sorted for CD8 (blue gate) and CD11b (orange gate) subsets and RNA prepared and analysed by RNA-Seq. (B) Heatmap showing the relative expression of the 50 most commonly defined and validated markers for CD8 and CD11b subsets. Data are presented as fold changes (CD11b/CD8), all of which were statistically significant with an associated p-value <0.05. Orange denotes genes that were increased in CD11b DCs while blue denotes genes that were decreased in CD11b DCs (and thus increased in CD8 DCs. (C) Overlap between genes that were significantly differentially expressed between CD8 and CD11b DCs in our dataset and in 9 previously published microarray datasets derived from splenic DC subsets (datasets 1–9 listed in Table S1). The significance of overlap between the gene list from our dataset and those from each of the published datasets was calculated using a hypergeometric test to assess the consistency/quality of our results. Data are presented as 1/p-value on a log scale with all overlaps reaching a significance cut-off <0.05.