Figure 2. Single-cell RNA-seq distinguishes cell cycle and other states among malignant cells.
(A) Estimation of the cell cycle state of individual malignant cells (circles) on the basis of relative expression of G1/S (x-axis) and G2/M (y-axis) gene-sets in a low-cycling (Mel79, top) and a high-cycling (Mel78, bottom) tumor. Cells are colored by their inferred cell cycle states, with cycling cells (red), intermediate (light red) and non-cycling cells (black); cells with high expression of KDM5B (Z-score>2) are marked in cyan filling. (B) IHC staining (40x magnification) for Ki67+ cells shows concordance with the signature-based frequency of cycling cells for Mel79 and Mel78 (as for other tumors; Fig S4C). (C) KDM5B/Ki67 staining (40x magnification) in corresponding tissue showing small clusters of KDM5B-high expressing cells negative for Ki67 (Fig. S4). (D) An expression program specific to Region 1 of Mel79, identified on the basis of multifocal sampling. The relative expression of genes (rows) is shown for cells (columns) ordered by the average expression of the entire gene-set. The region-of-origin of each cell is indicated in the top panel (Fig. S5).