Extended Data Fig. 3: Details of scRNA-seq analysis to annotate components of the melanoma TME.
a) Expression of marker genes of major cell lineages expected in the TME, shown on UMAP plots. b) Distribution of cell type signatures derived from murine melanoma scRNA-seq in spot types of the murine melanoma ST dataset. c) Selected cluster-specific markers used to annotate neural crest (NC) cell types/states. d) Violin plots of indicated gene expression signatures measured across NC clusters. e) Scatter plot of antagonistic MITF and AXL-driven gene expression signatures identified in human melanoma, across NC clusters in (d). f) Distribution of predicted cell cycle stages across NC clusters in (d). g) Pseudotime analysis of reclustered NC cells. Top, original neural crest clusters after re-integration, dimensionality reduction and UMAP embedding. Bottom, cell trajectories in pseudotime anchored in the melanocyte cluster (red dot). h) Representation of expression profiles of key genes across pseudotime in NC clusters. i) As in (c), for myeloid cells. j) Circos plots showing correspondence between myeloid cell clusters identified and myeloid cell identities in a published scRNA-seq datasets of murine subcutaneous sarcoma52. k) As in (j) in murine lung adenocarcinoma53. l) UMAP plot of lymphoid cells after re-integration, dimensionality reduction and UMAP embedding, labeled according to their original clusters (top) and annotations generated by reclustering (bottom). m) Selected markers used to annotate lymphoid cell types/states following reclustering in (l). n) UMAP representation of differential abundance analysis of cells in (l) performed with Milo. Cells are grouped into overlapping neighborhoods based on their K-nearest neighbor graph position, depicted as circles proportional in size to the number of cells contained, colored by log fold change of abundance between genotypes. Graph edge thickness is proportional to the number of cells shared between adjacent neighborhoods. o) Relative abundance across lymphoid clusters as annotated in (l) and (m), shown as percentage of total viable cells in each tumor.
