KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD144 (VE-Cadherin) microBeads | Miltenyi Biotec | Cat#130-097-857 |
| Anti-mouse IgG microbeads | Miltenyi Biotec | Cat# 130-048-401 |
| Rabbit polyclonal anti-ETS1 | Active Motif | Cat#39580; RRID: AB_2793266 |
| Mouse monoclonal anti-RNA pol II (Clone: 4H8) | Active Motif | Cat#39097; RRID: AB_2732926; |
| Rabbit monoclonal anti-CHD7 (Clone: D3F5) | Cell Signaling Technology | Cat#6505; RRID: AB_11220431 |
| Mouse monoclonal anti-NPR3 (Clone: OTI11B5) | OriGene | Cat# TA501079; RRID: AB_11127026 |
| Rabbit polyclonal anti-α-SMA | Abcam | Cat#ab5694; RRID: AB_2223021 |
| Rabbit polyclonal anti-Ki67 | Abcam | Cat# ab15580; RRID: AB_443209 |
| Mouse monoclonal anti-TNNT2 (Clone: 13- 11) | Thermo Scientific | Cat#MS-295-P; RRID: AB_61806; |
| Rabbit polyclonal anti-TNNT2 | Abcam | Cat#ab45932; RRID: AB_956386 |
| Mouse monoclonal anti-α-actinin (Clone: EA- 53) | Sigma-Aldrich | Cat#A7811; RRID: AB_476766 |
| Mouse monoclonal anti-CDH11 (Clone: 5B2H5) | Invitrogen | Cat#321700; RRID: AB_2533068 |
| Mouse monoclonal anti-CD31 (Clone: JC/70A) | Abcam | Cat#ab9498; RRID: AB_307284 |
| Mouse monoclonal anti-FN1 (Clone: IST-9) | Abcam | Cat#ab6328; RRID: AB_305428 |
| Mouse monoclonal anti-FN1- Xenopus laevis | Developmental studies hybridoma bank | Cat#4H2S; RRID: AB_2721949; |
| Donkey anti-Mouse secondary antibody, Alexa 488 | Invitrogen | Cat#A21202; RRID: AB_141607 |
| Donkey anti-Rabbit secondary antibody, Alexa 488 | Invitrogen | Cat#A21206; RRID: AB_2535792 |
| Donkey anti-Mouse secondary antibody, Alexa 594 | Invitrogen | Cat#A21203; RRID: AB_2535789 |
| Donkey anti-Rabbit secondary antibody, Alexa 594 | Invitrogen | Cat#A21207; RRID: AB_141637 |
| Bacterial and Virus Strains | ||
| GFP lentivirus | (Chen et al., 2017) | NA |
| ETS1 lentivirus | (Chen et al., 2017) | NA |
| Biological Samples | ||
| Human fetal heart samples | University of Washington Birth Defects Research Lab, USA. | NA |
| Human heart tissue sections | Sick Children and the Mount Sinai Hospital, University of Toronto, Canada. | NA |
| Chemicals, Peptides, and Recombinant Proteins | ||
| EGM-2 MV BulletKit (CC-3156 and CC-4147) | Lonza | Cat# CC-3162 |
| Essential 8 Medium | Gibco | Cat# A1517001 |
| mTeSR Medium | STEMCELL | Cat# 85850 |
| B-27 Supplement, minus insulin | Gibco | Cat# A1895601 |
| B-27 Supplement | Gibco | Cat# 17504044 |
| RPMI 1640 Medium | Gibco | Cat# 11875093 |
| RPMI 1640 Medium, minus glucose | Gibco | Cat# 11879020 |
| StemPro Accutase Cell Dissociation Reagent | Gibco | Cat# A11105-01 |
| DMEM, high glucose | Gibco | Cat# 11965118 |
| HBSS, calcium, magnesium, no phenol red | Gibco | Cat# 14025092 |
| Knockout™ DMEM | Gibco | Cat# 10829-018 |
| HEPES (1M) | Gibco | Cat# 15630080 |
| TrypLE™ Select Enzyme (10X) | Gibco | Cat# A1217703 |
| KnockOut™ Serum Replacement | Gibco | Cat# 10828028 |
| UltraPure 0.5M EDTA, pH 8.0 | Invitrogen | Cat# 15575-020 |
| 1X RBC lysis buffer | Invitrogen | Cat# 433357 |
| FcR Blocking Reagent, human | Miltenyi Biotec | Cat# 130-059-901 |
| Human VEGF-165 | Gemini | Cat#300196P100UG |
| Human FGF-basic 154 | Gemini | Cat#300113P050UG |
| CHIR-99021 (CT99021) HCl | Selleck Chemicals | Cat# S2924 |
| C59 | Selleck Chemicals | Cat# S7037 |
| Matrigel™ hESC-qualified Matrix, *LDEV- Free, 5mL | Corning | Cat# 354277 |
| Matrigel™ Membrane Matrix, Growth Factor Reduced | Corning | Cat# 354230 |
| Corning® BioCoat™ Laminin Plates | Corning | Cat# 354412 |
| Gelatin solution, Type B | Sigma-Aldrich | Cat# G1393-100mL |
| Fibronectin human plasma | Sigma-Aldrich | Cat# F2006 |
| Liberase TM | Sigma-Aldrich | Cat# 5401127001 |
| Y-27632 dihydrochloride | Tocris | Cat# 1254 |
| Recombinant Human TGF-β2 | PeproTech | Cat# 100-35B |
| Antigen Unmasking Solution, Tris-Based | Vector Lab | Cat# H-3301 |
| DNase I | Worthington | Cat# LK003172 |
| Belzer UW® Cold Storage Solution | Thermo Fisher | Cat# NC0952695 |
| Corning™ BioCoat™ Collagen IV Multiwell Plates | Thermo Fisher | Cat# 08-774-29 |
| Critical Commercial Assays | ||
| Corning® Transwell® polyester membrane cell culture inserts | Sigma-Aldrich | Cat# CLS3450-24EA |
| RNeasy Plus Micro Kit | Qiagen | Cat# 74034 |
| PowerUp SYBR Green Master Mix | Applied Biosystems | Cat# A25742 |
| High-Capacity RNA-to-cDNA™ Kit | Applied Biosystems | Cat# 4387406 |
| Deposited Data | ||
| Raw data files for scRNA-seq and bulk RNA- seq | NCBI GEO | GEO: GSE138979 |
| Experimental Models: Cell Lines | ||
| Control iPSC line 2 | CIRM Human Induced Pluripotent Stem Cell Repository | Cat# CW60359E |
| Control iPSC lines 1, 3, and 4 | Stanford University | NA |
| HLHS iPSC lines 1-3 | Mayo Clinic | NA |
| Experimental Models: Organisms/Strains | ||
| Xenopus laevis embryos | Nasco | Cat# LM00490 |
| Oligonucleotides | ||
| ON-TARGETplus Human ETS1 (2113) siRNA -SMARTpool | Dharmacon | Cat# L-003887-00-0005 |
| ON-TARGETplus Human CHD7 (55636) siRNA - SMARTpool | Dharmacon | Cat# L-025947-01-0005 |
| ON-TARGETplus Human FN1 (2335) siRNA - SMARTpool | Dharmacon | Cat# L-009853-00-0005 |
| ON-TARGETplus Human ARID1B (57492) siRNA - SMARTpool | Dharmacon | Cat# L-013970-01-0005 |
| ON-TARGETplus Human KMT2D (8085) siRNA - SMARTpool | Dharmacon | Cat# L-004828-00-0005 |
| Morpholino: MO-Ets1 5’-TAAGGTCTAGTGCAGCTTTCATGG C-3’ | This paper | NA |
| SYBR Green primers | See Table S5 | NA |
| Software and Algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/indeex.html |
| GraphPad Prism | GraphPad Software Inc | https://www.graphpad.com/scientific-software/prism/ |
| TrimGalore v0.4.4 | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | |
| STAR (2.5.4 a) | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| FeatureCounts | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| Bioconductor package DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Heatmap.2 in R package | https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2 | |
| 10X Chromium Single Cell Software Suite v2.1.1 | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/2.1/what-is-cell-ranger | |
| scRNA-seq dimensional reduction, clustering, visualization, differential expression detection- Seurat R packages | (Butler et al., 2018) | https://satijalab.org/seurat |
| Bioconductor package GeneAnswers | (Feng, 2018) | https://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html |
| Bedtools | https://bedtools.readthedocs.io/en/latest | |
| Homer annotatePeaks.pl script | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ngs/annotation.html |
| Customized R packages | This paper | https://github.com/Lei-Tian/HLHS |
| Other | ||
| QuadroMACS™ Separator and Starting Kits (LS) | Miltenyi Biotec | Cat# 130-091-051 |
| Bioruptor® Pico sonication device | Diagenode | Cat# B01060010 |