Extended Data Fig. 2: Differential gene expression analysis between fibroblasts and pericytes in the human breast.
From: Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis
a) Heatmap showing expression of top 20 marker genes specifically expressed in fibroblasts and pericytes from scRNA-seq dataset (rows=genes, columns=cells). Yellow represents a positive z-score, purple represents a negative z-score. b) Venn diagram illustrating the number of genes that are mutually or exclusively expressed in fibroblasts and pericytes. Selected marker genes for each category are shown. c) Volcano plot depicting differential gene expression analysis of fibroblasts (green) and pericytes (violet), the Wilcoxon rank sum test is used to determine differentially expressed genes, adjusted p values are determined using the Bonferroni method for multiple testing correction. d) Bar chart showing top 10 GO Terms enriched in all 367 fibroblast-specific genes. e) Bar chart showing top 10 GO Terms enriched in all 217 pericyte-specific genes. f) Dot plot illustrating mRNA expression levels of PDPN and PROCR by fibroblasts and pericytes, respectively. g) FACS plot gated on live cells, singlets, lin-, EpCAM− stromal cells showing distinct populations of PDPN + and PROCR + stromal cells. h) Gene expression analysis of FACS-isolated PROCRmid PDPN + stromal cells by qPCR for selected fibroblast-specific genes. Gene expression normalized to GAPDH and relative expression versus PDPN-PROCR + stromal cells from FACS is shown. Each bar graph shows three points (n = 3), each point represents 1 biologically independent patient’s averaged fold change of a technical triplicate (n = 3), Whisker plots represent the mean and the 25th and 75th quantiles. i) Gene expression analysis of FACS-isolated PROCR + PDPN- stromal cells by qPCR for selected pericyte-specific genes. Gene expression normalized to GAPDH and relative expression versus PROCRmidPDPN + stromal cells from FACS is shown. Each bar graph shows three points (n = 3), each point represents 1 biologically independent patient’s averaged fold change of a technical triplicate (n = 3), Whisker plots represent the mean and the 25th and 75th quantiles.
