Fig. 2

MS Cluster 1 is a quiescent stem-like cluster. A, B Cell cycle analysis was performed on MCF-7 MS using the Cell Cycle Scoring vignette provided by Seurat. A Bi-dimensional representations of 2974 single-cell transcriptomes colored by cell cycle phase (UMAP) and B cell cycle distribution for each cluster are shown. C An EdU assay was performed on MCF-7 MS. Representative pictures of MS stained for EdU (red) and DAPI (blue) are shown (bar = 50 µm) (D) A bar chart of EdU+ and EdU- cells presented as a percent of total number of cells from 11 MS is shown. E, F FEA was performed on the MS MCF-7 dataset with G0/quiescence-associated gene signatures with one representative example shown in a box plot. A detailed description of signatures is presented in Additional file 2: S. Table 6.1. AUC values are shown in a heatmap, and P-values are presented in Additional file 2: Supplemental Table 6.2. G Expression of genes associated with G0/Quiescence are represented in dot plots, with color representing expression level and size representing the percentage of cells in the cluster expressing the gene. H Cell cycle regression was performed using the Cell Cycle Regression vignette by Seurat. I, J Cell cycle phase and distribution are indicated after cell cycle regression of the MCF-7 MS dataset. K FEA was performed on MS MCF-7 dataset after cell cycle regression for stem cell-associated gene signatures from MsigDB. AUC values are shown in a heatmap, and P-values are presented in Additional file 2: Supplemental Table 7. (L) A Venn diagram shows percent of common DEGs derived from the MS Cluster 1 before and after cell cycle regression. M FEA was performed for the original MCF-7 MS Cluster 1 Signature on the MS MCF-7 dataset after cell cycle regression