(A) Schematic workflow. Epicardial stromal cells (EpiSC) and activated cardiac stromal cells (aCSC) were simultaneously collected from the surface and the myocardium of the isolated perfused heart …
Source data for EpiSC population cell counts summarized in Figure 1C.
(A) DoubletFinder tool was used to detect cell doublets with hybrid transcriptomes. (B) Heat map showing the expression of markers for cardiomyocytes (CM) and erythrocytes (Ery) used to identify …
Over-represented gene ontology (GO) terms in epicardial stromal cell (EpiSC) population marker genes as analyzed by Scillus.
Heat map showing the expression of the top 10 most differentially expressed genes in identified epicardial stromal cell (EpiSC) populations (color-coded according to their identity).
Feature plots and violin plots visualizing the expression levels of selected receptor–ligand pairs across different epicardial stromal cell (EpiSC) populations as identified by CellPhoneDB. (A) …
(A) Expression of epicardial progenitor cell markers proposed in the literature as visualized in feature and violin plots. (B) Upper panel: RNA in situ hybridization of epicardial stromal cell …
(A) UMAP plot of subclusters (Sub) of Wt1-expressing epicardial stromal cell (EpiSC)-7, -1, and -8. (B) UMAP plot of the subclustering with labeling according to previous identity. (C) Transfer of …
Expression of epicardial population markers identified in the developing zebrafish heart by Weinberger et al., 2020 visualized in the whole epicardial stromal cell (EpiSC) fraction (A and B) and in W…
UMAP plot of the epicardial stromal cell (EpiSC) fraction from lineage tracing experiments using Wt1CreERT2RosatdTomato mice with assignment of previously defined subclusters of Wt1-expressing EpiSC.
(A, B) Heat maps (A) and violin plots (B) of selected genes showing the expression of cardiogenic factors and Notch target genes. (C, D) Heat maps (C) and violin plots (D) of genes associated with …
(A) Canonical correlation analysis (CCA) space alignment of epicardial stromal cells (EpiSC), activated cardiac stromal cells (aCSC), and CSC single-cell RNA sequencing (scRNAseq) data in one UMAP …
(A) UMAP plot of clustered single-cell RNA sequencing (scRNAseq) data of the pooled activated cardiac stromal cell (aCSC) fraction (n = 24,470 single cells). Each point represents a single cell, and …
Source data for aCSC population cell counts summarized in Figure 4—figure supplement 1B.
(A) DoubletFinder tool was used to detect cell doublets with hybrid transcriptomes. (B) Heat map showing the expression of markers for mural cells, endothelial cells (EC), immune cells, …
Heat map showing the expression of the top 10 most differentially expressed genes in identified activated cardiac stromal cell (aCSC) populations (color-coded according to their identity).
(A) UMAP plot of clustered single-cell RNA sequencing (scRNAseq) data of the pooled cardiac stromal cell (CSC) fraction (n = 24,781 single cells). Each point represents a single cell and identified …
Source data for CSC population cell counts summarized in Figure 4—figure supplement 4B.
(A) DoubletFinder tool was used to detect cell doublets with hybrid transcriptomes. (B) Heat map showing the expression of markers for mural cells, cardiomyocytes (CM), endothelial cells (EC), glial …
Heat map showing the expression of the top 10 most differentially expressed genes in identified cardiac stromal cell (CSC) populations (color-coded according to their identity).
(A–C) Relative expression of epicardial and stromal cell markers (A), genes associated with HIF-1 signaling (B), and genes associated with cell proliferation (C) in cardiac stromal cell (CSC) and …
Source data for differentially expressed genes among EpiSC and CSC in CCA cluster A displayed in Figure 4—figure supplement 7D.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Mus musculus) | C57BL/6J | Janvier Labs | Strain name: C57BL/6JRj | |
Strain, strain background (M. musculus) | STOCK Wt1tm2(cre/ERT2)Wtp/J | The Jackson Laboratory; PMID:18568026 | Stock no. 010912; RRID:IMSR_JAX:010912 | |
Strain, strain background (M. musculus) | B6;129S6-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J | The Jackson Laboratory | Stock no. 007908; RRID:IMSR_JAX:007908 | |
Chemical compound, drug | Tamoxifen | Sigma-Aldrich | T5648 | |
Chemical compound, drug | 7AAD | BioLegend | 420404 | (1:100) |
Chemical compound, drug | Fixable Viability Dye eFluor 780 | eBioscience | 65–0865 | (1:100) |
Other | Collagenase CLS II | Biochrom | C2-22 | Enzyme blend; now available from Sigma-Aldrich, C2-BIOC |
Antibody | APC-conjugated rat monoclonal anti-CD31 | BioLegend | 102410, clone 390; RRID:AB_312905 | (1:100) |
Antibody | PE-Cy7 rat monoclonal anti-CD45 | BD Biosciences | 552848, clone 30-F11; RRID:AB_394489 | (1:400) |
Commercial assay or kit | RNAscope 2.5 HD Reagent Kit-RED | Advanced Cell Diagnostics | 322350 | |
Sequence-based reagent | RNAscope Probe Mm-Msln | Advanced Cell Diagnostics | 443241 | |
Sequence-based reagent | RNAscope Probe Mm-Wt1 | Advanced Cell Diagnostics | 432711 | |
Sequence-based reagent | RNAscope Probe Mm-Cd44 | Advanced Cell Diagnostics | 479191 | |
Sequence-based reagent | RNAscope Probe Mm-Ifit3 | Advanced Cell Diagnostics | 508251 | |
Sequence-based reagent | RNAscope Probe Mm-Sfrp2 | Advanced Cell Diagnostics | 400381 | |
Sequence-based reagent | RNAscope Probe Mm-Pcsk6 | Advanced Cell Diagnostics | 593361 | |
Sequence-based reagent | RNAscope Probe Mm-Top2a | Advanced Cell Diagnostics | 491221 | |
Sequence-based reagent | RNAscope Probe Mm-Dkk3 | Advanced Cell Diagnostics | 400931 | |
Software, algorithm | CellRanger | 10x Genomics | ||
Software, algorithm | Seurat | PMID:29608179 | RRID:SCR_007322 | |
Software, algorithm | DoubletFinder | PMID:30954475 | RRID:SCR_018771 | |
Software, algorithm | Scillus | https://github.com/xmc811/ Scillus Xu, 2021 | ||
Software, algorithm | GOrilla | PMID:19192299 | RRID:SCR_006848 | |
Software, algorithm | Velocyto.py | PMID:30089906 | RRID:SCR_018167 | |
Software, algorithm | CellPhoneDB | PMID:32103204 | RRID:SCR_017054 | |
Software, algorithm | SCENIC | PMID:28991892 | RRID:SCR_017247 |
Average gene expression levels in EpiSC, aCSC, and CSC populations.
Genes with significantly enriched expression among EpiSC, aCSC, and CSC populations.
Selected ligand–receptor interactions between EpiSC populations as predicted by CellPhoneDB.
Average gene expression levels in subclusters of Wt1-expressing EpiSC populations.
Genes with significantly enriched expression among subclusters of Wt1-expressing EpiSC populations.
Genes with significantly enriched expression in group I and group II populations vs group III populations.
Average gene expression levels in clusters from CCA space alignment of EpiSC, aCSC, and CSC with separation in EpiSC, aCSC, and CSC, including p-values of differential expression.
Genes with significantly enriched expression among clusters from CCA space alignment of EpiSC, aCSC, and CSC.