(A and B) Overview of lineage tracing and scRNAseq approach in embryonic and adult mice. (C–K) Unbiased clustering of embryonic coronary ECs at the indicated time points and the contribution of …
(A and B) tdTomato localization in sections BmxCreER;RosatdTomato hearts at e17.5 (A) and adult (B). Dashed yellow lines indicate the borders of the tissue sections. Dashed red line indicates the …
(A and B) Uniform Manifold Approximation and Projections (UMAPs) showing expression of selected EC subtype markers in e12 ECs (A) and e17.5 ECs (B). (C and D) Breakdown of cell types as percentage …
(A, B, and C) Uniform Manifold Approximation and Projections (UMAPs) showing expression of selected coronary EC subtype markers in coronary ECs at e12 (A), e17.5 (B) and adult (C). Scale bar from (C)…
(A) Uniform Manifold Approximation and Projection (UMAP) showing unbiased clustering of e17.5 mouse coronary ECs before the removal of cycling cells. (B) UMAP showing unbiased clustering of e17.5 …
(A) Uniform Manifold Approximation and Projections (UMAPs) showing expression of selected coronary EC subtype markers in the adult coronary EC dataset from Figure 1.
(A) Heatmap showing expression of the top 30 (by p-value) Endo-defining genes (enriched in the Endo compared to the SV) and the top 30 (by p-value) SV-defining genes (enriched in the SV compared to …
(A) Uniform Manifold Approximation and Projection (UMAP) showing expression of canonical Endo (Cdh11) and SV (Vwf, Bmp4) markers in heart endothelial cells (ECs) at e12. (B, C, and D) Expression of …
(A) Uniform Manifold Approximation and Projection (UMAP) showing expression of selected coronary EC subtype markers in a previously published dataset. (B and C) Expression in e12 dataset of genes …
(A) Heatmap showing expression of selected genes enriched in either Cap1 or Cap2 at e17.5 (E = coronary cells from endocardium [Endo]-enriched sample, S = coronary cells from sinus venosus …
Counts of Car4+ and Car4- endothelial cells in sections of BmxCreER hearts at e17.5.
(A) Uniform Manifold Approximation and Projections (UMAPs) showing expression of selected flow-induced genes from Kumar et al., 2014, in e17.5 coronary endothelial cells (ECs). (B) Quantification of …
(A) Uniform Manifold Approximation and Projections (UMAPs) showing expression of Endo-enriched genes manually determined to be expressed in a higher percentage of proposed septum cells (as shown in F…
(A) Overview of lineage tracing and ischemia-reperfusion (I/R) injury approach in adult mice. (B) Example of how EdU localization highlights mid-myocardial injury region. Yellow arrowheads indicate …
Counts of proliferating and non-proliferating endothelial cells in sections of adult BmxCreER hearts after injury.
(A) Overview of scRNAseq approach for three human fetal hearts. (B and C) Uniform Manifold Approximation and Projections (UMAPs) of all major PECAM1+ EC subtypes collected (B) and the non-cycling …
(A) Immunofluorescence for CD36 and Erg in a section from a 14-week human fetal heart. (B) Uniform Manifold Approximation and Projections (UMAPs) showing expression of CD36 in human coronary ECs as …
(A) Uniform Manifold Approximation and Projections (UMAPs) showing unbiased clustering of cells isolated from each individual human fetal heart. (B) Trajectory analysis of human coronary EC at each …
(A) Reference mapping showed that e17.5 mouse endothelial cells (ECs) from Figure 5g were assigned to all three human artery subsets. (B) Trajectory analysis of human coronary ECs using …
(A) Heatmap showing expression of selected genes enriched in human artery clusters. (B and C) Regulon scores from SCENIC analysis for TFs enriched in all human and mouse artery clusters (B) and for …
(A) UMAP plots showing clustering of e17.5 dataset at multiple resolutions up to 0.6 as well as expression of the top 5 DEGs (by average log-fold change) between newly divided clusters. The clusters …
Endo-specific genes | SV-specific genes |
---|---|
Cdkn1c | Cldn11 |
Tmem108 | Aplnr |
Nrk | Agr2 |
Fabp5 | Bmp4 |
Cdh11 | Hoxa5 |
Cd81 | Gm13889 |
Irx5 | Zfp503 |
H19 | Hotairm1 |
Hand2 | Rassf9 |
Adgrg6 | Mmrn1 |
Maged2 | Pcdh17 |
Ccnd2 | Tox |
Plvap | Slco3a1 |
Igf2 | Tspan13 |
Dok | Nr2f2 |
Col13a1 | Fst |
Tm4sf1 | Cd36 |
Igf2r | Cldn5 |
Gm1673 | Aqp1 |
Blvrb | Hoxb4 |
Gsta4 | Khdrbs3 |
Rap2a | Kitl |
Gatm | Wnt16 |
Olfml3 | Limch1 |
Sdpr | Ahr |
Ece1 | Edn1 |
Plagl1 | Lamp5 |
Prr15 | Cav1 |
Igfbp4 | Ddah1 |
Ccnd3 | Tbx5 |
List of all differentially expressed genes between e12 endocardium (Endo) and sinus venosus (SV) sorted by Wilcoxon rank sum test.
Bolded genes are also differentially expressed between Cap1 and Cap2.
Raw p-value | Average log-fold change | % Endo cells expressing | % SV cells expressing | Adjusted p-value | Higher fold change in Cap1 versus Cap2 comparison? | |
---|---|---|---|---|---|---|
tdTomato | 1.91E-238 | 0.39378511 | 0.452 | 0 | 5.35E-234 | |
Gt(ROSA)26Sor | 2.43E-153 | –0.634801942 | 0.568 | 0.837 | 6.81E-149 | |
Anxa1 | 4.24E-109 | 0.553933954 | 0.804 | 0.53 | 1.19E-104 | |
Igf2 | 6.74E-93 | –0.357191579 | 0.99 | 0.999 | 1.89E-88 | |
Timp4 | 1.28E-88 | –0.632710228 | 0.447 | 0.766 | 3.58E-84 | Yes |
Fmo1 | 8.34E-70 | –0.351754806 | 0.231 | 0.511 | 2.34E-65 | Yes |
Txnip | 2.09E-67 | –0.37131915 | 0.851 | 0.933 | 5.85E-63 | Yes |
Aplnr | 5.42E-67 | –0.40125981 | 0.677 | 0.863 | 1.52E-62 | Yes |
Car4 | 1.68E-65 | –0.595662824 | 0.347 | 0.62 | 4.70E-61 | Yes |
Aqp7 | 3.33E-62 | –0.368823615 | 0.345 | 0.63 | 9.31E-58 | Yes |
Apoe | 1.19E-60 | 0.302862096 | 0.307 | 0.09 | 3.34E-56 | |
Cd36 | 8.58E-59 | –0.308565577 | 0.97 | 0.997 | 2.40E-54 | Yes |
Igfbp5 | 1.84E-57 | 0.4602195 | 0.258 | 0.064 | 5.15E-53 | |
Fabp5 | 6.53E-54 | 0.30861622 | 0.999 | 1 | 1.83E-49 | Yes |
1810011O10Rik | 1.08E-52 | –0.340249285 | 0.907 | 0.963 | 3.04E-48 | Yes |
Aqp1 | 9.79E-47 | –0.471913791 | 0.54 | 0.729 | 2.74E-42 | Yes |
Gap43 | 7.23E-38 | 0.34418651 | 0.523 | 0.331 | 2.02E-33 | Yes |
Sat1 | 1.99E-37 | 0.394143816 | 0.753 | 0.63 | 5.59E-33 | Yes |
Cd63 | 3.81E-36 | 0.33008301 | 0.758 | 0.611 | 1.07E-31 | Yes |
Igfbp3 | 3.45E-34 | 0.640208849 | 0.634 | 0.468 | 9.66E-30 | Yes |
Tm4sf1 | 1.38E-32 | 0.302207793 | 0.982 | 0.94 | 3.87E-28 | |
Maged2 | 4.03E-32 | 0.323885527 | 0.845 | 0.757 | 1.13E-27 | |
Ly6c1 | 1.32E-31 | –0.301696479 | 0.845 | 0.93 | 3.70E-27 | Yes |
Rbp1 | 1.26E-15 | 0.432393695 | 0.757 | 0.69 | 3.52E-11 | Yes |
LV | Septum | |
---|---|---|
heart1 | 0.874 | 0.853 |
heart2 | 0.864 | 0.819 |
SLC14A1 |
GABBR2 |
NRN1 |
EPHA3 |
ADMTSL1 |
A2M |
PRND |
GRIA2 |
KCNN3 |
SERPINE2 |
LPCAT2 |
LGALS3 |
APOA1 |
SYNJ2 |
OCIAD2 |
PRICKLE2 |
CTNND1 |
IFITM2 |
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Mus musculus) | BmxCreER | Mouse Genome Informatics | MGI: 5513853; RRID: IMSR_TAC:14081 | |
Strain, strain background (Mus musculus) | RosatdTomato | The Jackson Laboratory | Stock No: 007909; RRID: IMSR_JAX:007909 | |
Strain, strain background (Mus musculus) | CD1 | Charles River Laboratories | Strain code: 022; RRID: IMSR_CRL:022 | |
Biological sample (Homo sapiens) | Primary fetal heart tissue | Collected at Stanford from elective terminations | ||
Antibody | Rat anti- APC/Cy7 Cd45 (rat monoclonal) | Biolegend | Cat #: 103116; RRID: AB_312981 | (1:50) |
Antibody | Rat anti- APC Pecam1 (rat monoclonal) | Biolegend | Cat #: 102410; RRID: AB_312905 | (1:50) |
Antibody | Rat anti- APC-Cy7 Ter119 (rat monoclonal) | Biolegend | Cat #: 116223; RRID: AB_2137788 | (1:50) |
Antibody | Mouse anti- Pacific Blue CD235a (mouse monoclonal) | Biolegend | Cat #: 349107; RRID: AB_11219199 | (1:50) |
Antibody | Mouse anti- FITC CD36 (mouse monoclonal) | Biolegend | Cat #: 336204; RRID: AB_1575025 | (1:50) |
Antibody | Mouse anti- APC-Cy7 PECAM1 (mouse monoclonal) | Biolegend | Cat #: 303119; RRID: AB_10643590 | (1:50) |
Antibody | Mouse anti- Pacific Blue CD45 (mouse monoclonal) | Biolegend | Cat #: 304021; RRID: AB_493654 | (1:50) |
Antibody | Mouse anti- PerCP-Cy5.5 CD235a (mouse monoclonal) | Biolegend | Cat #: 349110; RRID: AB_2562706 | (1:50) |
Antibody | Mouse anti-PerCP-Cy5.5 CD45 (mouse monoclonal) | Biolegend | Cat #: 304028; RRID: AB_893338 | (1:50) |
Antibody | Rabbit anti-Erg (rabbit monoclonal) | Abcam | Cat #: ab92513; RRID: AB_2630401 | (1:200) |
Antibody | Goat anti-Car4 (goat polyclonal) | R&D | Cat #: AF2414; RRID: AB_2070332 | (1:200) |
Antibody | Rabbit anti-Smmhc (rabbit polyclonal) | Proteintech | Cat #: 21404–1-AP; RRID: AB_10732819 | (1:100) |
Antibody | Mouse anti-Cldn5 (mouse monoclonal) | Invitrogen | Cat #: 35–2500; RRID: AB_2533200 | (1:200) |
Peptide, recombinant protein | Collagenase IV | Worthington | Cat #: LS004186 | |
Peptide, recombinant protein | Dispase | Worthington | Cat #: LS02100 | |
Peptide, recombinant protein | DNase I | Worthington | Cat #: LS002007 | |
Commercial assay or kit | RNEasy Mini Kit | Qiagen | Cat #: 74,104 | |
Commercial assay or kit | iScript Reverse Transcription Supermix | Bio-Rad | Cat #: 1708840 | |
Commercial assay or kit | Roche DIG RNA Labeling kit | Millipore Sigma | Cat #: 11175025910 | |
Commercial assay or kit | RNAscope Multiplex Fluorescent V2 assay kit | Advanced Cell Diagnostics | Cat #: 323,100 | |
Commercial assay or kit | Click-iT EdU Imaging kit | Thermo Fisher Scientific | Cat #: C10086 | |
Chemical compound, drug | Tamoxifen | Sigma-Aldrich | Cat #: T5648 | |
Chemical compound, drug | 4-OH Tamoxifen | Sigma-Aldrich | Cat #: H6278 | |
Software, algorithm | Seurat v3 | https://doi.org/10.1016/j.cell.2019.05.031 | RRID: SCR_007322 | |
Software, algorithm | bcl2fastq | illumina | RRID: SCR_015058 | |
Software, algorithm | cutadapt 2.7 | https://doi.org/10.14806/ej.17.1.200 | RRID: SCR_011841 | |
Software, algorithm | Cell Ranger v3.1.0 | 10× Genomics | RRID: SCR_017344 | |
Software, algorithm | STAR v2.7.1a | https://doi.org/10.1093/bioinformatics/bts635 | RRID: SCR_004463 | |
Software, algorithm | Subread v1.6.0 | https://doi.org/10.1093/nar/gkt214 | RRID: SCR_009803 | |
Software, algorithm | heatmaply | http://dx.doi.org/10.1093/bioinformatics/btx657 | https://github.com/talgalili/heatmaply (Galili, 2021) | |
Software, algorithm | biomaRt | 10.18129/B9.bioc.biomaRt | RRID: SCR_019214 | |
Software, algorithm | PAGA | https://doi.org/10.1186/s13059-019-1663-x | https://github.com/theislab/paga (Thesis Lab, 2019) | |
Software, algorithm | RNA velocity | 10.1038/s41586-018-0414-6 | RRID: SCR_018168; RRID: SCR_018167 | |
Software, algorithm | Slingshot | https://doi.org/10.1186/s12864-018-4772-0 | RRID: SCR_017012 | |
Software, algorithm | SCENIC | 10.1038/nmeth.4463 | RRID: SCR_017247 | |
Software, algorithm | FIJI | doi:10.1038/nmeth.2019 | RRID: SCR_002285 | |
Software, algorithm | QuPath | https://doi.org/10.1038/s41598-017-17204-5 | RRID: SCR_018257 | |
Software, algorithm | Prism 8 | GraphPad Software | RRID: SCR_002798 | |
Other | TINAGL1 RNA probe | Advanced Cell Diagnostics | Cat #: 857221-C2 |