Fig. 2: Transcriptional programming of migrated human LCs.

a Dominant biological processes and pathways enriched in genes expressed at varying levels in steady-state migrated LCs. Gene ontology analysis for each expression level (Fragments Per Kilobase of transcript per Million mapped reads, FPKM) interval determined by RNA-seq was performed using ToppGene on-line tool⁷⁸. Line denotes median value in the interval. Top unique Biological processes are shown for each interval, significance denoted by FDR (Benjamini-Hochberg) corrected P-value is shown. The x-axis shows consecutive cut-offs for each interval in gene expression levels. Source data are provided as a Source Data file. b Overlaps between reported cross-presentation (373 genes) and antigen processing (212 genes) signatures, and genes expressed in migrated LC > 10 FPKM. c Intracellular expression of SQSTM1 and TRIM21 measured by flow cytometry. Steady-state (blue) and migrated (red) LCs. Representative histograms followed by quantitative analysis n = 4 independent donors, unpaired t test, line denotes median value. Source data are provided as a Source Data file. d TNF stimulation (24 h) of human LCs induces genes involved in antigen trafficking (red), processing (purple) and cross-presentation (blue). Expression levels of three biological replicates (TMM normalised gene expression levels, scaled in rows). Source data are provided as a Source Data file. e Enrichment of immune activation genes upregulated during a time course of TNF stimulation: left: early induced genes, peak expression at 2 h, Cluster 3, right: late induced genes, peak expression at 24 h. Median of three biological replicates, normalised expression levels. Stars denote genes belonging to antigen presentation in class I, MSigBD, Broad Institute. Source data are provided as a Source Data file.