KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-human SSEA-3 | BD Biosciences | (clone MC-6310) RRID:AB_1645542 |
| Anti-human SSEA-4 | BD Biosciences | (clone MC813–70) RRID:AB_2033991 |
| Anti-human Tra-1–60 | BD Biosciences | (clone TRA-1–60) RRID:AB_10565983 |
| Anti-human TRA-1–81 | BD Biosciences | (clone TRA-1–81) RRID:AB_1645493 |
| Anti-human EpCAM (CD326) | BioLegend | (clone 9C4) RRID:AB_756082 |
| Anti-human CD56 | BD Biosciences | (clone NCAM16.2) RRID:AB_400025 |
| Anti-human CD30 | BD Biosciences | (clone BerH8) RRID:AB_393541 |
| Anti-human CD3 (BV510) | BD Biosciences | (clone UCHT1) RRID:AB_2732053 |
| Anti-human CD3 (APC) | BD Biosciences | (clone SK7) RRID:AB_400513 |
| Anti-human CD4 (Per-CP) | BD Biosciences | (clone SK3) RRID:AB_400282 |
| Anti-human CD4 (PE-Cy7) | BD Biosciences | (clone SK3) RRID:AB_396897 |
| Anti-human CD8α (PE) | BD Biosciences | (clone SK1) RRID:AB_400005 |
| Anti-human CD8α (Per-CP) | BD Biosciences | (clone SK1) RRID:AB_400280 |
| Anti-human CD8α (APC-Cy7) | BD Biosciences | (clone SK1) RRID:AB_400383 |
| Anti-human CD8β | BD Biosciences | (clone 2ST8.5H7) RRID:AB_1645747 |
| Anti-human CD5 | BD Biosciences | (clone UCHT2) RRID:AB_2737700 |
| Anti-human CD7 | BD Biosciences | (clone M-T701) RRID:AB_2738544 |
| Anti-human TCR αβ | BD Biosciences | (clone T10B9.1A-31) RRID:AB_2738437 |
| Anti-human TCR γδ | BD Biosciences | (clone B1) RRID:AB_396061 |
| Anti-human TCR γδ | BD Biosciences | (clone 11F2) RRID:AB_2827402 |
| Anti-human NKG2A | R&D Systems | (clone 131411) RRID:AB_2132978 |
| Anti-human NKG2D (CD314) | BD Biosciences | (clone 1D11) RRID:AB_10896282 |
| Anti-human NKp44 (CD336) | BD Biosciences | (clone p44–8) RRID:AB_647239 |
| Anti-human NKP46 (CD335) | BioLegend | (clone 9E2) RRID:AB_2561649 |
| Anti-human CD19 | BD Biosciences | (clone SJ25C1) RRID:AB_396893 |
| Anti-human CD16 | BD Biosciences | (clone NKP15 ) RRID:AB_400317 |
| Anti-human Fas L (CD178) | BD Biosciences | (clone NOK-1) RRID:AB_2738713 |
| Anti-human CD62L (PE) | BD Biosciences | (clone SK11) RRID:AB_400205 |
| Anti-human CD62L (FITC) | BD Biosciences | (clone SK11) RRID:AB_400302 |
| Anti-human CD45RA | BD Biosciences | (clone HI100) RRID:AB_398468 |
| Anti-human CD45RO | BD Biosciences | (clone UCHL1) RRID:AB_395883 |
| Anti-human EGFR (APC) | BioLegend | (clone AY13) RRID:AB_11150410 |
| Anti-human EGFR (PE-Cy7) | BioLegend | (clone AY13) RRID:AB_2562159 |
| Anti-human CD28, InVivoMab | Bio X Cell | (clone 9.3) RRID:AB_2687729 |
| Anti- human CD27 | BD Biosciences | (clone M-T271) RRID:AB_395834 |
| Anti-human CD28 (APC-H7) | BD Biosciences | (clone CD28.2) RRID:AB_11154032 |
| Anti-human CD279 (PD-1) | ThermoFisher Scientific | (clone eBioJ105) RRID:AB_2573976 |
| Anti-human LAG3 /CD223 | Lifespan | (clone 17B4) RRID:AB_1650048 |
| Anti-human TIM-3 | R&D Systems | (clone 344823) RRID:AB_2232901 |
| Anti-human IgG Fc | Abcam | Abcam # ab98622, RRID:AB_10673586 |
| Pan p44/42 MAPK (phosphorylated Erk1/2) antibody | Cell Signaling Technology | Polyclonal, Cat# 9101, RRID:AB_331646 |
| Pan p44/42 MAPK (Erk1/2) antibody | Cell Signaling Technology | (clone 3A7) RRID:AB_10695739 |
| Anti-human, -mouse phospho-PLCγ1 (Tyr783) antibody | Cell Signaling Technology | (clone D6M9S) RRID:AB_2728690 |
| Anti-human, -mouse, -monkey phospho-PLC 1 (Ser1248) antibody | Cell Signaling Technology | (clone D25A9) RRID:AB_10890863 |
| Anti-human, -rat, -mouse PLCγ1 | Cell Signaling Technology | Polyclonal, Cat# 2822, RRID:AB_2163702 |
| Anti-human, -mouse phospho-Zap-70 (Tyr319)/Syk (Tyr352) | Cell Signaling Technology | (clone 65E4) RRID:AB_2218658 |
| Anti-human, -mouse, anti-CD3ζ (pY142) | BD Biosciences | (clone K25–407.69) RRID: AB_647307 |
| Bacterial and virus strains | ||
| NEB 5-alpha Competent E. coli | NEB | C2987 |
| Biological samples | ||
| PBMC from healthy donor | This paper | N/A |
| Primary B-ALL patient samples | This paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Proleukin (aldesleukin), rhIL-2 | Novartis Oncology | NCD 65483–116-07 |
| rhIL-15 | CellGenix, US Operations | 1413–050 |
| Activin A | R&D Systems | 338-AC-010 |
| rhBMP-4 | R&D Systems | 314-BP-010 |
| rhVEGF | R&D Systems | 293-VE-010 |
| rhFGF-basic | Peprotech | AF-100–18B |
| ROCK inhibitor, Y-27632 dihydrochloride | StemCell Technologies | 72304 |
| TGFβ-RI inhibitor, SB-431542 | StemCell Technologies | 72234 |
| rhFlt3-Ligand | Peprotech | AF-300–19 |
| rhIL-7 | Peprotech | AF-200–07 |
| rhTPO | Peprotech | 300–18 |
| rhSCF | Peprotech | AF-300–07 |
| MEM α, with nucleosides | GIBCO | 12571063 |
| Fetal bovine serum, defined, heat-inactivated | HyClone | SH30070.03IH |
| X-VIVO 15 Serum-free Hematopoietic Cell Medium | Lonza | BEBP04–744Q |
| EGM-2, Endothelial Cell Growth Medium-2 Bullet Kit | Lonza | CC-3162 |
| RPMI 1640 Medium with L-Glutamine and HEPES | Lonza | 12–115F |
| GLutaMAX Supplement | ThermoFisher Scientific | 35050061 |
| 2-Mercaptoethanol, 55 mM | ThermoFisher Scientific | 21985023 |
| MEM Non-Essential Amino Acids Solution (100X) | ThermoFisher Scientific | 11140050 |
| L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate | Sigma | A8960 |
| Phosphate-buffered saline | Irvine Scientific | 9240 |
| Penicillin-Streptomycin (100X) | Lonza | 17602E |
| mTeSR1 | StemCell Technologies | 85850 |
| DMEM/F12, with HEPES | ThermoFisher Scientific | 11330057 |
| Matrigel hESC-Qualified Matrix, LDEV-free | Corning | 354277 |
| ReLeSR | StemCell Technologies | 5872 |
| CloneR | StemCell Technologies | 5889 |
| StemPro Accutase Cell Dissociation Reagent | ThermoFisher Scientific | A1110501 |
| DNase I | Zymo Research | E1010 |
| B-27 Supplement (50X) | ThermoFisher Scientific | 17504–044 |
| TrypLE Express Enzyme (1X) | ThermoFisher Scientific | 12605010 |
| Protamine sulfate | APP Pharmaceuticals | NDC 63323–229-05 |
| XenoLight D-luciferin potassium salt | PerkinElmer | 122799 |
| Hanks’ Balanced Salt Solution, w/o Ca++, Mg++ | GIBCO | 14175103 |
| 0.05% Trypsin/0.53mM EDTA in HBSS w/o Ca++, Mg++ | Corning | MT25051CI |
| Brefeldin A Golgi Plug | BD Biosciences | 555029 |
| Critical commercial assays | ||
| Leukocyte Alkaline Phosphatase Kit | Sigma | 86R-1KT |
| IOTest beta Mark TCR Vβ Repertoire Kit | Beckman Coulter | IM3497 |
| TCRB T-Cell Clonality Assay Kit | Invivoscribe | 12000011 |
| CD34 MicroBead Kit UltraPure | Miltenyi Biotec | 130–100-453 |
| EasySep Human CD56 Positive Selection Kit II | Stem Cell Technologies | 17855 |
| EasySep Human EpCAM Positive Selection Kit II | Stem Cell Technologies | 17846 |
| Dynabeads™ Human T-Expander CD3/CD28 | ThermoFisher Scientific | 11141D |
| RNeasy Micro Kit | Qiagen | 74004 |
| Quick-RNA Microprep Kit | Zymo Research | R1050 |
| EZ DNA Methylation-Lightning Kit | Zymo Research | D5030 |
| Fixation/Permeabilization Solution Kit | BD Biosciences | 554714 |
| Luminex Cytokine Mouse Magnetic 10-Plex Panel | ThermoFisher Scientific | LMC0001M |
| Millicell Cell Culture Insert, 30 mm, hydrophilic PTFE, 0.4 μm | Millipore Sigma | PICM0RG50 |
| Deposited data | ||
| RNA expression data by high throughput sequencing | This paper | NCBI GEO: GSE193422 |
| Experimental models: Cell lines | ||
| T cell derived iPSC lines | this paper | N/A |
| Fibroblast derived iPSC line | ATCC | DYS0100, ACS-1019 |
| MS5-hDLL4-eGFP | Gay Crooks’ lab | N/A |
| NALM6.ffluc.eGFP | this paper | N/A |
| NALM6.ffluc.eGFP_CD19KO | this paper | N/A |
| Raji.ffluc.eGFP | this paper | N/A |
| Raji.ffluc.eGFP_CD19KO | this paper | N/A |
| 3T3_CD19 | This paper | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) | Jackson Laboratory | Strain #005557 |
| Oligonucleotides | ||
| Primers for EF1α promoter PCR and sequencing, see Extended Table 2 | This paper | N/A |
| Recombinant DNA | ||
| CD19-CAR_pHIV (CD19-CAR) | Forman lab | N/A |
| CLTX-CAR_pHIV (CLTX-CAR) | Forman lab | N/A |
| hOCT3/4-shp53_pCXLE | addgene, gift from Shinya Yamanaka | RRID:Addgene_27077 |
| hSK_pCXLE (SOX2, KLF4) | addgene, gift from Shinya Yamanaka | RRID:Addgene_27078 |
| hUL_pCXLE (L-MYC, LIN28) | addgene, gift from Shinya Yamanaka | RRID:Addgene_27080 |
| EBNA_pCXLE | addgene, gift from Shinya Yamanaka | RRID:Addgene_37624 |
| Software and algorithms | ||
| GraphPad Prism GraphPad Software | GraphPad Software | https://www.graphpad.com/ |
| Flowjo | Tree Star Inc. | https://www.flowjo.com/solutions/flowjo |
| Zen | Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html |
| BZ-X800 Analyzer | Keyence | https://www.keyence.com/landing/microscope/lp_fluorescence.jsp |
| R package “DESeq2” (v.3.10) |
R | https://www.r-project.org |
| Cluster (v.3.0) (clustering algorithms) |
Human Genome Center Institute of Medical Science, University of Tokyo | http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm |
| JavaTreeView (v.1.1.6r4) | Stanford University School of Medicine | http://jtreeview.sourceforge.net/ |
| “edgeR” (v.3.28.0) | R | http://bioconductor.org/packages/release/bioc/html/edgeR.html |
| “ggplot2” (v.3.2.1) | R | https://cran.r-project.org/web/packages/ggplot2/index.html |
| GSEA (v.4.0.3). (gene set enrichment analysis) | Broad Institute | https://www.gsea-msigdb.org/gsea/index.jsp |
| BioRender | BioRender.Inc | https://app.biorender.com/ |
| Other | ||
| N/A | ||