REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE-Cy7 Mouse anti-Human CD34 (Clone 581)	BD Biosciences	Catalog No: 560710, RRID AB_1727470
APC Mouse anti-Human CD43 (Clone 1G10)	BD Biosciences	Catalog No: 560198, RRID AB_1645460
Brilliant Violet 711 Mouse anti-Human CD45 (Clone HI30)	Biolegend	Catalog No: 304050, RRID AB_2563466
APC Mouse anti-Human APNLR (APJ) (Clone 72133)	R&D system	Catalog No: FAB856A RRID AB_ 2044604
PE-Cy7 Mouse anti-Human CD73 (Clone AD2)	Biolegend	Catalog No: 344010, RRID AB_2561542
APC Mouse anti-Human CD44 (Clone G44-26)	BD Biosciences	Catalog No: 559942, RRID AB_398683
PE Mouse anti-Human CD140a (PDGFRα) (Clone 16A1)	Biolegend	Catalog No: 323506, RRID AB_2268113
PE Mouse anti-Human CD105 (Clone 43A3)	Biolegend	Catalog No: 323206, RRID AB_755958
PE Mouse anti-Human CD140b (PDGFRβ) (Clone 18A2)	Biolegend	Catalog No: 323606, RRID AB_2268134
PE Mouse anti-Human SSEA-4 (Clone MC-813-70)	Biolegend	Catalog No: 330406, RRID AB_1089206
Brilliant Violet 605 Mouse anti-Human CD31 (Clone WM59)	Biolegend	Catalog No: 303122, RRID AB_2562149
Brilliant Violet 605 Mouse anti-Human CD5 (Clone UCHT2)	BD Biosciences	Catalog No: 563945, RRID AB_2738500
PE Mouse anti-Human CD7 (Clone M-T701)	BD Biosciences	Catalog No: 555361, RRID AB_395764
PE-Cy7 Mouse anti-Human CD4 (Clone SK3)	BD Biosciences	Catalog No: 557852, RRID AB_396897
APC Mouse anti-Human CD8 (Clone RPA-T8)	BD Biosciences	Catalog No: 555369, RRID AB_398595
Brilliant Violet 421 Mouse anti-Human CD8b (Clone 2ST8.5H7)	BD Biosciences	Catalog No: 742390, RRID AB_AB_2740746
V450 Mouse anti-Human CD3 (Clone UCHT1)	BD Biosciences	Catalog No: 561812, RRID AB_1645570
APC Mouse Anti-Human CD71 (Clone L01.1)	BD Biosciences	Catalog No: 341028, RRID AB_400560
PE Mouse Anti-Human CD235a	BD Biosciences	Catalog No: 555570, RRID AB_395949
PE Mouse Anti-Human CD235a (Clone HI264)	Biolegend	Catalog No: 349106, RRID AB_10640739
Brilliant Violet 421 Mouse anti-human CD41a (Clone HIP8)	Biolegend	Catalog No: 303730, RRID AB_2629627
FITC Mouse Anti-Human CD14 (Clone M5E2)	BD Biosciences	Catalog No: 555397, RRID AB_395798
PE Mouse Anti-Human CD45 (Clone HI30)	BD Biosciences	Catalog No: 555483, RRID AB_395875
APC Mouse Anti-Human CD11b (Clone ICRF44)	BD Biosciences	Catalog No: 550019, RRID AB_398456
PE Mouse Anti-Human CD16 (Clone 3G8)	BD Biosciences	Catalog No: 555407, RRID AB_395807
APC Mouse Anti-Human CD13 (Clone WM15)	BD Biosciences	Catalog No: 557454, RRID AB_398624
APC Mouse Anti-Human CD33 (Clone WM53)	BD Biosciences	Catalog No: 551378, RRID AB_398502
Brilliant Violet 605 Mouse anti-Human TNF-α (Clone MAb11)	Biolegend	Catalog No: 502932, RRID AB_10898321
PE-Cy7 Mouse anti-human IFN-γ (Clone 4S.B3)	Biolegend	Catalog No: 502536, RRID AB_11125368
eBioscience™ Fixable Viability Dye eFluor™ 450	Thermo Fisher Scientific	Catalog No: 65-0863-14
CD4 Micro-Bead Kit, human	Miltenyi Biotec	Catalog No: 130-045-101
CD34 Micro-Bead Kit, human	Miltenyi Biotec	Catalog No: 130-046-702
Peptide HLA-A∗02:01 Mart-1 ELAGIGILTV	MBL	Catalog No: SP0009
iTAg Tetramer/PE – HLA-A∗02:01 Mart-1	MBL	Catalog No: TB-0009-1
Mouse anti-alpha-Fetoprotein/AFP Monoclonal Antibody (1:200) (Clone 189502)	R&D system	Catalog No: MAB1368, RRID AB_357658
Rabbit anti-PDGFRb Monoclonal Antibody (1:200) (Clone 42G12)	Abcam	Catalog No: ab69506, RRID AB_1269704
Rabbit anti-CD31 Monoclonal Antibody (1:100) (Clone EPR3094)	Abcam	Catalog No: ab76533, RRID AB_1523298
Rabbit anti-CD34 Monoclonal Antibody (1:100) (Clone EP373Y)	Abcam	Catalog No: ab81289, RRID AB_1640331
Mouse Anti-CD43 Monoclonal Antibody (1:300) (W3/13)	Abcam	Catalog No: ab22351, RRID AB_447013
Alexa 488-conjugated anti-Mouse IgG (H + L)	Thermo Fisher Scientific	Catalog No: A11001, RRID AB_2534069
Alexa 555-conjugated anti-Rabbit	Thermo Fisher Scientific	Catalog No: A21429, RRID AB_2535850
Alexa 647-conjugated anti-Mouse	Abcam	Catalog No: ab150115, RRID AB_2687948
Alexa 488-conjugated anti-Rabbit	Abcam	Catalog No: ab150081, RRID AB_2734747
TotalSeq™-A0251 anti-human Hashtag 1 Antibody	Biolegend	Catalog No: 394601, RRID AB_2750015
TotalSeq™-A0252 anti-human Hashtag 2 Antibody	Biolegend	Catalog No: 394603, RRID AB_2750016
Chemicals, peptides, and recombinant proteins
Hoechst 33342 trihydrochloride trihydrate	Thermo Fisher Scientific	Catalog No: H3570
ProLong™ Gold Antifade Mountant	Thermo Fisher Scientific	Catalog No: P36930
Fixation/Permeabilization Solution Kit with BD GolgiStop™	BD Cytofix/Cytoperm	Catalog No: 554715
Recombinant Human BMP-4	R&D systems	Catalog No: 314-BP
Recombinant Human FGF2	R&D Systems	Catalog No: 233-FB
Recombinant Human IL3	R&D Systems	Catalog No: 203-IL
Recombinant Human IL6	R&D Systems	Catalog No: 206-IL
Recombinant Human IL7	R&D Systems	Catalog No: BT-007
Recombinant Human Flt3-Ligand	R&D Systems	Catalog No: 427-FL
Recombinant Human stem cell factor (SCF)	R&D Systems	Catalog No: 255-SC 050/CF
Recombinant Human VEGF	PeproTech	Catalog No: 100-20
Recombinant Human Thrombopoietin (TPO)	R&D Systems	Catalog No: 288-TP
Recombinant Human PDGF-BB	R&D Systems	Catalog No: 220-BB
Erythropoietin	Amgen	EPOGEN®
Dexamethasone	VETone	Catalog No: 501012
Estradiol	Pfizer	DEPO®-ESTRADIOL
Insulin	Lilly	Humulin® R U-100
holo-Transferrin human	Sigma-Aldrich	Catalog No: T4132-500MG
Bovine Serum Albumin (Roche)	Millipore Sigma	Catalog No: 10735078001
CHIR99021	Tocris Bioscience	Catalog No: 4953
Activin A	PeproTech Inc.	Catalog No: 120–14P
Phorbol 12-myristate 13-acetate (PMA)	Sigma-Aldrich	Catalog No: P8139
Zymosan An S. cerevisiae BioParticles, FITC conjugate	Thermo Fisher Scientific	Catalog No: Z2841
Dihydrorhodamine 123 (DHR)	Thermo Fisher Scientific	Catalog No: D632
Giemsa stain Solution	Thermo Fisher Scientific	Catalog No: 10092-013
Gibco MEM α, nucleosides, powder (α MEM)	Thermo Fisher Scientific	Catalog No: 11900024
Iscove’s Modified Dulbecco’s Medium (for Macrophage differentiation)	Thermo Fisher Scientific	Catalog No: 12440-053
Iscove’s Modified Dulbecco’s Medium (for erythroid cell differentiation)	Sigma-Aldrich	Catalog No: I3390
Fetal Bovine Serum (FBS), Embryonic Stem Cell Qualified	R&D Systems	Catalog No: S10250H
Recombinant Human Macrophage Colony Stimulating Factor (M-CSF)	PeproTech	Catalog No: 300-25
Interferon γ (IFN-γ)	Horizon Therapeutics	Actimmune®
Busulfan	Otsuka America Pharmaceutical	Busulfex® IV
Y-27632 dihydrochloride	R&D Systems	Catalog No: 1254
DMEM/F12 - Dulbecco’s Modified Eagle Medium	Thermo Fisher Scientific	Catalog No: 11320033
Granulocyte-Colony Stimulating Factor (G-CSF)	Amgen	Neupogen® Filgrastim
Corning Matrigel matrix	Corning	Catalog No: 354230
PLTGold® Human Platelet Lysate (heparin-free)	Mill Creek Life Sciences	Catalog No: PLTGold100R
StemFit C02	Ajinomoto Co., Inc	Kindly provided from Ajinomoto Co., Inc
StemFit for differentiation	Nacalai USA	Catalog No: AS401
Stemfit Basic02	Nacalai USA	Catalog No: BASIC02
CELLBANKER	Amsbio	Product code: 11910
TrypLE™ Express Enzyme	Thermo Fisher Scientific	Catalog No: 12605010
Liberase™ TM Research	Roche	Catalog No: 5401127001
DNase I	Roche	Catalog No: 10104159001
0.1% Gelatin in Water	STEMCELL Technologies	Catalog No: 07903
Able Bioreactor System Controller and Motor 30 mL	REPROCELL	ABBWDW-1013
Able Bioreactor Magnetic Stir System Base 30mL	REPROCELL	ABBWBP03N0S-6
Ultra-low attachment plates: 96 well, U bottom	S-BIO	Catalog No: MS-9096UZ
Anti-Adherence Rinsing Solution	STEMCELL Technologies	Catalog No: 07010
AggreWell™400 (6-well plate)	STEMCELL Technologies	Catalog No: 34425
AggreWell™800 (24-well plate)	STEMCELL Technologies	Catalog No: 34815
Critical commercial assays
MethoCult GF H4034 Starter Kit	STEMCELL Technologies	Catalog No: 04064
RNeasy Plus Mini Kit	Qiagen	Catalog No: 74134
TruSeq Stranded Total RNA Library Prep	Illumina	Catalog No: 20020596
Chromium Next GEM Single Cell 3′ Kit	10X Genomics	Catalog No: 1000268
Deposited data
Raw Bulk RNA-seq and scRNA-seq data, count matrices	This paper	GEO: GSE157140
Experimental models: Cell lines
OP9/N-DLL1	Riken Bioresource center	RRID:CVCL_B220
OP9/N	Riken Bioresource center	RRID:CVCL_B219
NCRM5-AAVS1-CAG-EGFP	iPSC core, NHLBI, NIH	https://www.nhlbi.nih.gov/science/ipsc-core
NCRM5	iPSC core, NHLBI, NIH	https://www.nhlbi.nih.gov/science/ipsc-core
Mart1-iPSC	Kawamoto Lab	https://www.infront.kyoto-u.ac.jp/en/laboratory/lab14/
SCD-iPSC	Tisdale Lab	https://www.nhlbi.nih.gov/science/cellular-and-molecular-therapeutics
Experimental models: Organisms/strains
NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice	The Jackson Laboratory	Strain #: 005557
Software and algorithms
Graphpad Prism 9	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
FlowJo software	FlowJo, LCC	https://www.flowjo.com/
Cutadapt 1.18	Martin, 201187	https://github.com/marcelm/cutadapt/
STAR 2.6.1	Dobin et al., 201388	https://github.com/alexdobin/STAR
RSEM 1.2.31	Li and Dewey, 201189	https://github.com/deweylab/RSEM
edgeR 3.28.1	Robinson et al., 201090	https://bioconductor.org/packages/release/bioc/html/edgeR.html
GSEA 4.0.3	Mootha et al., 200391; Subramanian et al., 200592	https://www.gsea-msigdb.org/gsea/index.jsp
Cell Ranger 3.1.0	10X Genomics, Inc.	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat_4.0.5	Butler et al., 201893; Stuart et al., 201994	https://satijalab.org/seurat/
Other
CliniMACS CD34 GMP Micro-Beads	Miltenyi Biotec	Catalog No: 170-076-711
CliniMACS Plus Instrument	Miltenyi Biotec	Catalog No: 151-01
ImmunoSEQ (TCR seq)	Adaptive Biotechnologies	N/A