Fig. 5.

mLN SCs modulate subset composition and transcriptional signature of resident DCs. Indicated LNs were transplanted to the popliteal fossa of SPF-housed mice. Eight to sixteen weeks later, single cell suspensions were generated by enzymatic digestion. a–d Single cell suspensions were analyzed using flow cytometry. a Exemplary dotplot of viable Lin⁻ cells from transplanted LN. (b) Exemplary dotplot of subsets from resDCs and migDCs from indicated LNs. c–d Scatterplot shows frequencies of indicated subsets among migDCs (c) and resDCs (d); data pooled from two to three independent experiments (n = 12–16). e resDCs were isolated from indicated LNs. RNA-seq^L and subsequent analysis was performed. Colored numbers in scatterplots represent DEGs for the respective pair-wise comparisons of resDCs (|log₂(FC)| ≥ 1 and q-value ≤ 0.05). On the x-axis log₂FC of gene expression from resDCs (endogenous LNs) is plotted. On the y-axis log₂(FC) of gene expression from resDCs of transplanted mLN-SPF vs. pLN-SPF is plotted. f Heatmap of expression of genes persistently down- (pink dot, left) or up-regulated (blue dot, right) in resDCs isolated from transplanted mLN-SPF. Numbers in brackets indicate average log₂(RPKM) expression of respective genes across all experimental groups. Data pooled from two to three independent experiments (n = 3–8). migDC migratory dendritic cell (Lin⁻CD11c⁺MHCII^high), resDC resident dendritic cell (Lin⁻CD11c^highMHCII⁺), Lin CD3⁺CD45R⁺Ly6G⁺F4/80^high, FC fold-change, RPKM reads per kilobase of exon length per million mapped reads, Endo endogenous, Tx transplanted