KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-human CD3 | Biolegend | (clone UCHT1) |
| Anti-human CD4 | Biolegend | (clone RPA-T4) |
| Anti-human CD43 | BD Bioscience | (clone 1G10) |
| Anti-human CD5 | Biolegend | (clone UCHT2) |
| Anti-human CD7 | BD Bioscience | (clone M-T701) |
| Anti-human CD8a | Biolegend | (clone SK1) |
| Anti-human CD8b | BD Bioscience | (clone 2ST8.5H7) |
| Anti-human CD25 | Biolegend | (clone BC96) |
| Anti-human CD27 | Biolegend | (clone O323) |
| Anti-human CD28 | Biolegend | (clone CD28.2) |
| Anti-human CD31 | Biolegend | (clone WM59) |
| Anti-human CD326 (EPCAM) | Biolegend | (Clone 9C4) |
| Anti-human CD34 | Biolegend | (clone 581) |
| Anti-human CD38 | Biolegend | (clone HIT2) |
| Anti-human CD45 | Biolegend | (clone HI30) |
| Anti-human CD45RA | Biolegend | (clone HI100) |
| Anti-human CD45RO | Biolegend | (clone UCHL1) |
| Anti-human CD56 | Biolegend | (clone HCD56) |
| Anti-human CD62L | Biolegend | (clone DREG-56) |
| Anti-human CD90 | Biolegend | (clone 5E10) |
| Anti-human CD107a | Biolegend | (clone H4A3) |
| Anti-human CD144 | BD Bioscience | (clone 55–7H1) |
| Anti-human CCR7 | Biolegend | (clone G043H7) |
| Anti-human interferon γ | Biolegend | (clone 4S.B3) |
| Anti-human IL-2 | Biolegend | (clone MQ1–17H12) |
| Anti-human TCRαβ | Biolegend | (clone IP26) |
| Anti-human TCRγδ | Biolegend | (clone B1) |
| Anti-human TNFα | Biolegend | (clone Mab11) |
| Anti-human Vβ13.1 | Biolegend | (clone H131) |
| Anti-human CD137 (4–1BB) | Biolegend | (clone 4B4–1) |
| Anti-human Ki67 | Biolegend | (clone ki-67) |
| Anti-human TdT | Biolegend | (clone 41A) |
| Anti-mouse CD29 | Biolegend | (clone HMβ1–1) |
| Anti-mouse Ter119 | Biolegend | (clone Ter119) |
| Anti-mouse CD45 | Biolegend | (clone 30-F11) |
| Anti-GFP | Biolegend | (clone FM264G) |
| Rat IgG1, x isotype ctrl | Biolegend | (clone RTK2071) |
| AlexaFluor-594-conjugated donkey anti-mouse IgG (H+L) | Jackson immunoResearch | Cat. 715–515-151 |
| AlexaFluor-488-conjugated donkey anti-rat IgG (H+L) | Jackson immunoResearch | Cat. 712–485-153 |
| Bacterial and Virus Strains | ||
| pCCL-c-MNDU3-hDLL4 (lentivirus) | This paper | N/A |
| pCCL-c-MNDU3-hDLL4-P2A-eGFP (lentivirus) | This paper | N/A |
| pCCL-UBC-opt1G4-mTagBFP2 (lentivirus) | This paper | N/A |
| Biological Samples | ||
| Postnatal human Thymi | CHLA | N/A |
| Cord Blood CD34+ cells | UCLA | N/A |
| Fetal human thymus | UCLA | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| rhIL-2 | Peprotech | Cat. 200–02 |
| rhBMP4 | R&D Systems | Cat. 314-BP-010 |
| rhVEGF | R&D Systems | Cat. 298-VS-005 |
| rhFGF | R&D Systems | Cat. 233-FB-025 |
| ROCK inhibitor Y-27632 dihydrochloride | Tocris Bioscience | Cat. 1254 |
| TGF-βRI inhibitor SB-431542 | Tocris Bioscience | Cat. 1614 |
| rhFLT3L | Peprotech | Cat. 300–19 |
| rhIL-7 | Peprotech | Cat. 200–07 |
| rhTPO | Peprotech | Cat. 300–18 |
| rhSCF | Peprotech | Cat. 300–07 |
| DNAse I | Sigma | Cat. 9003–98-9 |
| Collagenase/dispase | Roche | Cat. 11097113001 |
| Collagenase Type IV | StemCell Technologies | Cat. 07909 |
| B27 supplement | Gibco | Cat. 17504–044 |
| Accutase | Innovative Cell Technologies | Cat. AT-104 |
| TrypLE™ Express | Gibco Life technologies | Cat. 12604–013 |
| Annexin V | Biolegend | |
| TruStain FcX | Biolegend | Cat. 422302 |
| DAPI | Life technologies | Cat. D1306 |
| Formaldehyde | Sigma-Aldrich | Cat. F8775 |
| Vectashield Antifade Mounting Medium | Vector Laboratories | Cat. H1000 |
| Critical Commercial Assays | ||
| CD34 MicroBead Kit UltraPure | Miltenyi | Cat. 130–100-453 |
| IOTest Beta Mark TCR V Kit | Beckman coulter | Cat. IM3497 |
| iTAg Tetramer/APC - HLA-A*02:01 NY-ESO-1 (SLLMWITQC) | MBL International | Cat. T01065 |
| ImmunoSEQ | Adaptive Biotechnologies | https://www.adaptivebiotech.com/immunoseq/products/ |
| CD8+ T Cell Isolation Kit | Miltenyi | Cat. 130–096-495 |
| Cell Stimulation Cocktail (plus protein transport inhibitors) | eBioscience | Cat. 00–4975-03 |
| Intracellular Fixation & Permeabilization Buffer Set | eBioscience | Cat. 88–8824-00 |
| Foxp3 staining Buffer Set | eBioscience | Cat. 00–5523-00 |
| True-Nuclear Transcription Factor Buffer Set | BIolegend | Cat. 424401 |
| CFSE proliferation assay | Biolegend | Cat. 423801 |
| antiCD3/CD38 beads | ThermoFisher Scientific | Cat. 111.61D |
| RNeasy Micro kit | Qiagen | Cat. 74004 |
| SMARTer Stranded Total RNA-Seq (Pico) Kit | Clonetech | Cat. 635005 |
| Zombie UV™ Fixable Viability Kit | Biolegend | Cat. 423107 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE116015 |
| Experimental Models: Cell Lines | ||
| H1 ESC line | WiCell | https://www.wicell.org/ |
| UCLA3, UCLA6 ESC lines | UCLA PSC core | Diaz Perez., et al 2012 |
| ESI-017 ESC line | ESI BIO | https://www.esibio.com/media/wysiwyg/esibio/documents/esicells/WEB_Rev_B_ESI-017_Data_Sheet.pdf |
| iPSC (DMD 1001 R1) line | UCLA PSC core | Hazim et al., 2017 |
| H1-opt1G4-mTagBFP2 hESC line | This paper | N/A |
| MS5-hDLL1 | Seet et al., 2017 | N/A |
| MS5-hDLL4 | This paper | N/A |
| MS5-hDLL4-eGFP | This paper | N/A |
| K562-CD80/83/137L-HLA-A*02:01/B2M/NY-ESO-1157–165 aAPC | This paper | N/A |
| K562-HLA-A*02:01/B2M/NY-ESO-1157–165 aAPC | This paper | N/A |
| K562-HLA-A*02:01/B2M/ MART-126–35 aAPC | This paper | N/A |
| Experimental Models: Organisms | ||
| Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | The Jackson Laboratory | JAX: 005557 |
| Software and Algorithms | ||
| FlowJo | Tree Star Inc. | https://www.flowjo.com/solutions/flowjo |
| UMAP (Uniform Manifold Approximation and Projection for Dimension Reduction | McInnes et al., 2018 | https://umap-learn.readthedocs.io/en/latest/ |
| GraphPad Prism | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| bcl2fastq2 (v2.17) | Illumina | https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2–20.html |
| The STAR ultrafast universal RNA-seq aligner v2.5.2b | Dobin et al., 2013 | N/A |
| DESeq2 | Love et al.,2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Metascape | Metascape | http://metascape.org |
| Cytoscape | Shannon et al.,2003 | http://www.cytoscape.org/ |
| Matlab | The MathWorks, Inc | https://www.mathworks.com/products/matlab.html |
| R | R | https://www.R-project.org/ |
| Zen | Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html |