Fig. 3: scRNA-seq analysis of migrated human LCs.
From: Genomic programming of IRF4-expressing human Langerhans cells
a UMAP plot of 950 migrated LCs (ScanPy, Leiden r = 0.2, n_pcs = 4, n_neighbours = 10, 2464 highly variable genes (min_mean = 0.0125, max_mean = 6, min_disp = 0.6) defines three major clusters of LCs. b Pseudotrajectory analysis of the transcriptomes of 950 migrated LCs (ScanPy, diffmap: Leiden r = 0.2, n_pcs = 4, n_neighbours = 10). Cells are colour coded for clusters as in panel a. c Gene ontology analysis for marker genes (n = 100) representative of indicated cluster, performed using ToppGene. –log(10) Benjamini-Hochberg corrected P-values are shown for cluster-specific processes. Source data are provided as a Source Data file. d Barplots displaying frequency and amplitude expression of indicated gene transcripts. Bars are colour coded for cells as in panel a. Representative uniformly expressed genes characteristic of LCs (top panel), genes involved in antigen presentation and processing (middle panels) and genes functioning in oxidative phosphorylation (bottom panel) are displayed. Each bar shows CPTT (counts per ten thousand) normalised expression level of indicated transcript in a given LC.
