Fig. 1

Intercellular heterogeneity in TNBC quantified by scRNA-seq. a Workflow showing collection and processing of fresh TNBC primary tumors for generating scRNA-seq data. b Heatmap of the 1189 cells that passed quality control, with columns representing cells and rows representing established gene expression markers for the cell types indicated on the left, clustered separately for each of the six TNBC cases. The upper bar denotes inferred high cycling (pink) and low cycling (gray) cells, as identified by quantifying the expression of a set of relevant genes (see Supplementary Methods). Bottom bar denotes cells collected in the presence/absence of CD45 + cell depletion. c Bar plot depicting the distribution of the 1112 cells assigned to specific cell types, by patient. d Bar plot depicting the high cycling/low cycling distribution of the 1112 cells, by patient. e Proliferation characteristics for two representative TNBC patients, depicted as either the inferred cycling status of single cells (left) or immunohistochemistry staining for Ki67 (right). Scale bars represent 50 µm. A cell is considered high cycling if it has high G1/S or G2/M scores, as identified by quantifying the expression of a set of relevant genes. The two ways of quantifying proliferation show good concordance