Fig. 1

Single-cell RNA sequencing reveals two putative stem-like cell population clusters in mammospheres derived from ER+ breast cancer cell lines. A Different numbers of MCF-7 cells, cultured in standard 2D or mammosphere conditions, were injected into the mammary gland of athymic mice. The incidence of tumor formation was determined over 6 weeks. A significant difference in stem cell frequency, based on the tumor incidence per condition, was determined by ELDA (P < 0.05). ND, not detected. B scRNA-seq was conducted on MS derived from MCF-7 cells. Bi-dimensional representation of 2974 single-cell transcriptomes is shown (UMAP). C The percentage of cells in each cluster relative to the total number of cells is shown. D FEA was performed 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 3. E 5739 single-cell transcriptomes derived from MCF-7 MS and T47D MS were integrated and represented bi-dimensionally. F The distribution of MCF-7 and T47D cells in each cluster relative to the total cell number is shown. G FEA for stem cell-associated gene signatures was performed on the MCF-7 and T47D integrated dataset. AUC values are shown in a heatmap, and P-values are presented in Additional file 2: Supplemental Table 4. H, I FEA was performed for the gene signatures derived from the DEGs of MCF-7 MS Cluster 1 (H) and MCF-7 MS Cluster 2 (I) Signatures on the MCF-7 and T47D integrated dataset. Box plots show signatures scores per integrated cluster with significant AUC and P-values indicated in grey