KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal to cardiac troponin T | ICC: abcam clone 1F11 Flow: Thermo Fisher clone: 3–11 |
ICC: ab10214 Flow: MS-295-p |
| Mouse monoclonal to a-Actinin (clone EA-53) | sigma | A7811–2ml |
| Rabbit polyclonal to Connexin 43 polyclonal | abcam | Ab11370 |
| Rabbit polyclonal to GFP | Thermo Fisher | A11122 |
| Donkey anti-mouse IgG(H+L), AlexaFluor647 conjugated | Jackson Lab | 715–695-151 |
| Donkey anti-rabbit IgG(H+L), AlexaFluor488 conjugated | Jackson Lab | 711–545-152 |
| Biotin anti-Thy1.2 | Invitrogen | 13–0903-85 |
| Bacterial and Virus Strains | ||
| E.coli: HB101 | Promega | |
| Biological Samples | ||
| Human cardiac tissue from a male patient | Duke Human Heart Repository | https://sites.duke.edu/dhhr/ |
| Neonatal P1.5 mouse hearts | This paper | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Poly-l-lysine | Electron microscopy science (EMS) | 19321-B |
| DMEM | Corning | 10–013-CV |
| FBS | Millipore | TMS-013-B |
| Non-essential amino acids | Corning | 25–025-CI |
| Penicillin/streptomycin | Corning | 30–002-CI |
| PEG6000 | Sigma | 81255–2.5g |
| 0.05% Trypsin | Corning | 25–052-CI |
| M199 | Corning | 10–060-CV |
| Polybrene | Millipore | TR-1003-G |
| SurCoat | Celltron | SC-9035 |
| RPMI1640 | gibco | 11875–093 |
| B27 supplement | gibco | 17504–044 |
| BSA | Hyclone | SH3057402 |
| GlutaMAX | gibco | 35050–061 |
| Gelatin | sigma | G1393–100ml |
| Collagenase type II | Worthington | LS004176 |
| HBSS | Corning | 21–022-CV |
| EDTA | sigma | E5134 |
| Anti-Biotin Microbeads | Miltenyi Biotec | 130–090-485 |
| TRIzol | Life technologies | 15596018 |
| 32% paraformaldehyde | EMS | 15714 |
| Triton X-100 | Acros | 21568–2500 CAS 900293–1 |
| Hoechst 33342 | Life Technologies | H3570 |
| Isopropanol | Fisher | M-15805 |
| Puromycin | Thermo Fisher | A1113803 |
| Critical Commercial Assays | ||
| NanoFect transfection Reagent | Alstem | NF101 |
| neonatal cardiomyocytes isolation system | Worthington Biochemical Corporation | 130–101-372 |
| Fixation/Permeabilization Solution | BD Biosciences | 51–2090KZ |
| Perm/Wash Solution | BD Biosciences | 51–2091KZ |
| SuperScript III Reverse Transcriptase kit | Invitrogen | 18080093 |
| Power SYBR Green PCR Master Mix | Applied Biosystems | 1710515 |
| DNeasy Blood & Tissue Kits | Qiagen | 69504 |
| EZ DNA Methylation-Gold Kit | Zymo Research | D5005 |
| EpiMark Hot Start Taq DNA Polymerase | NEB | M0490S |
| NearIR live/dead dye | Thermo Fisher Scientific | L10119 |
| Carboxyfluorescein succinimidyl ester (CFSE) dye | Thermo Fisher Scientific | 65–0850-84 |
| Ambion Array Control spike-ins | Thermo Fisher | AM1780 |
| External RNA Controls Consortium (ERCC) RNA spike-in Mix 1 | Ambion | 4456740 |
| C1™ Single-Cell mRNA Seq IFC, 17–25 µm—10 IFCs | Fluidigm | 100–6042 |
| C1™ Single-Cell Reagent Kit for mRNA Seq | Fluidigm | 100–6201 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GEO: GSE106888 |
| Human reference genome NCBI build 37, GRCh37 | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| Experimental Models: Cell Lines | ||
| Human: PlatE | Cell Biolabs | RV-101 |
| Human: 293LTV Cell Line | Cell Biolabs | LTV-100 |
| Human: ESC H9 derived fibroblasts: H9F | Fu et al., 2013 | |
| Human: primary cardiac fibroblasts: HCF1 | This paper | |
| Human: primary cardiac fibroblasts: HCF2 | Cheng et al., 2012 | |
| Experimental Models: Organisms/Strains | ||
| Mouse: aMHC-GFP transgenic CD1 | Ieda et al., 2010 | |
| Oligonucleotides | ||
| See primer sequences for RT-PCR in Table S2 | This paper | |
| Primers for bisulfite sequencing | Fu et al., 2013 | |
| Recombinant DNA | ||
| pMXs-MEF2C | Fu et al., 2013 | |
| pMXs-GATA4 | Fu et al., 2013 | |
| pMXs-TBX5 | Fu et al., 2013 | |
| pMXs-ESRRG | Fu et al., 2013 | |
| pMXs-MESP1 | Fu et al., 2013 | |
| pMXs-MYOCD | Fu et al., 2013 | |
| pBabe-GATA4 | Nam et al., 2013 | |
| pBabe-HAND2 | Nam et al., 2013 | |
| pBabe-MEF2C | Nam et al., 2013 | |
| pBabe-TBX5 | Nam et al., 2013 | |
| pBabe-MYOCD | Nam et al., 2013 | |
| pBabe-MESP1 | Nam et al., 2013 | |
| pBabe-miR-1 | Nam et al., 2013 | |
| pBabe-miR-133 | Nam et al., 2013 | |
| pMXs-puro-hMGT | This paper | |
| pMXs-puro-LacZ | Cell Biolabs | |
| pMXs-puro-dsRed | Wang et al., 2015a | |
| pMXs-GFP | Wang et al., 2015a | |
| pMXs-tdTomato | Ziqing Liu et al. | |
| TroponinT-GCaMP5-Zeo | Addgene #46027 | |
| pCMV-VSV-G | Addgene #8454 | |
| pUMVC | Addgene #8449 | |
| psPAX2 | Addgene #12260 | |
| MG2.G | Addgene #12259 | |
| pGEMT | Promega | |
| See list of shRNA cloned in pLKO.1 vector in Table S2. | Sigma | |
| Software and Algorithms | ||
| ImageJ (Fiji version) | NIH | https://imagej.net/Fiji/Downloads |
| FlowJo | ||
| GraphPad Prism | ||
| liteCam HD | RSUPPORT | |
| EVOS microscope system | Invitrogen | |
| Bisulfite Sequencing DNA Methylation Analysis (BISMA) | Rohde et al., 2010 | |
| R 3.3.2 | https://www.r-project.org/ | |
| SLICER | Welch et al., 2016 | https://github.com/jw156605/SLICER |
| SCnorm | Bacher et al., 2017 | https://bioconductor.org/packages/release/bioc/html/SCnorm.html |
| SINGuLAR Analysis Toolset | Fluidigm | https://www.fluidigm.com/software/ |
| reCAT | Zehua Liu et al., 2017 | https://github.com/tinglab/reCAT |
| DESeq2 | Love et al., 2014 | |
| TargetScan tool | Agarwal et al., 2015 | http://www.targetscan.org/vert_71 |
| miRDB | Wong and Wang, 2015 | http://mirdb.org |
| DAVID GO | https://david.ncifcrf.gov/ | |
| REVIGO | Supek et al., 2011 | http://revigo.irb.hr |
| HTSeq | Anders et al., 2015 | http://www.huber.embl.de/users/anders/HTSeq |
| velocyto.R | La Manno et al., 2018 | https://github.com/velocytoteam/velocyto.R)) |
| Other | ||