Fig. 3

Single-cell RNA sequencing (scRNA-seq) and gene differential expression analysis. a Schematic depiction of the origination of sequenced samples. b Gene set enrichment analysis (GSEA) of gene sets enriched in BCSCs compared with those in non-BCSCs. FDR, false discovery rate; NES, normalized enrichment score. c The dot plot (left) shows differentially expressed genes between BCSCs and non-BCSCs. The red dots represent 74 BCSC highly expressed genes with a false discovery rate (FDR) < 0.05 and a fold change > 2. Heatmap (right) illustrates the hierarchical clustering of BCSCs and non-BCSCs showing the 74 genes, with previously reported BCSC-associated genes highlighted with red color. d The validation result of BCSC highly expressed genes using bulk-cell RNA-seq. Heatmap (left) shows the relative expression of BCSC highly expressed genes, and scatter plots (right) illustrate the high correlation of the results between scRNA-seq and bulk-cell RNA-seq