REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
BV421 Anti-human CD45 antibody, for flow cytometry of differentiated hPSCs	Thermo Fisher	404-0459-42
FITC Anti-human CD14 antibody, for flow cytometry of differentiated hPSCs	Biolegend	301804
FITC Anti-human CD33 antibody, for flow cytometry of differentiated hPSCs	Biolegend	303304
PE Anti-human CD235A/GPA antibody, for flow cytometry of differentiated hPSCs	Thermo Fisher	12-9987-82
APC Anti-human CD71 antibody, for flow cytometry of differentiated hPSCs	Thermo Fisher	17-0719-42
APC Anti-mouse/human CD11b antibody, for flow cytometry of differentiated hPSCs	Biolegend	101212
PE Cy7 Anti-human CD68 antibody, for flow cytometry of differentiated hPSCs	Thermo Fisher	25-0689-42
Alexa Fluor 700 Anti-human CD56 antibody, for flow cytometry of differentiated hPSCs	Biolegend	318316
APC Anti-human CD56 antibody, for flow cytometry of differentiated hPSCs	Biolegend	318310
APC-Cy7 Anti-human NKp46 antibody, for flow cytometry of differentiated hPSCs	Biolegend	331950
APC-Cy7 Anti-human CD336 (NKp44) antibody, for flow cytometry of differentiated hPSCs	Biolegend	325123
PE Anti-human CD314 (NKG2D) antibody, for flow cytometry of differentiated hPSCs	Biolegend	320805
PE Anti-human CD94 antibody, for flow cytometry of differentiated hPSCs	Biolegend	305506
PE-Cy7 Anti-human CD16 antibody, for flow cytometry of differentiated hPSCs	Biolegend	302016
APC-Cy7 Anti-human CD3 antibody, for flow cytometry of differentiated hPSCs	Biolegend	344818
PE Anti-human CD3 antibody, for flow cytometry of differentiated hPSCs	Biolegend	300441
Alexa Fluor 700 Anti-human CD3 antibody, for flow cytometry of differentiated hPSCs	Biolegend	300423
PE Anti-human CD5 antibody, for flow cytometry of differentiated hPSCs	Biolegend	300608
APC Anti-human CD7 antibody, for flow cytometry of differentiated hPSCs	BD Biosciences	653311
APC-Cy7 Anti-human CD4 antibody, for flow cytometry of differentiated hPSCs	Biolegend	300518
PE-Cy7 Anti-human CD8 antibody, for flow cytometry of differentiated hPSCs	Biolegend	344712
APC Anti-human TCRα/β antibody, for flow cytometry of differentiated hPSCs	Biolegend	306718
PE-Cy7 Anti-human CD10 antibody, for flow cytometry of differentiated hPSCs	Biolegend	312214
APC Anti-human CD19 antibody, for flow cytometry of differentiated hPSCs	Biolegend	302212
PE Anti-human CD144 antibody, for flow cytometry of differentiated hPSCs	BD Biosciences	560410
FITC Anti-human CD144 antibody, for flow cytometry of differentiated hPSCs	BD Biosciences	560411
APC Anti-human DLL4 antibody, for flow cytometry of differentiated hPSCs	Biolegend	346508
PE-Cy7 Anti-human CD34 antibody, for flow cytometry of differentiated hPSCs	Biolegend	343516
APC Anti-human CD43 antibody, for flow cytometry of differentiated hPSCs	BD Biosciences	560198
PE-Cy7 Anti-human CD45 antibody, for flow cytometry of differentiated hPSCs	BD Biosciences	557748
Alexa Fluor 488 Anti-human CD45 antibody, for flow cytometry of differentiated hPSCs	Biolegend	304017
eFluor 450 Anti-human CD34 antibody, for flow cytometry of human cord blood HSPCs	Thermo Fisher	48-0349-42
FITC Anti-Human CD90 antibody, for flow cytometry of human cord blood HSPCs	BD Biosciences	555595
PE Anti-human CD45RA antibody, for flow cytometry of human cord blood HSPCs	Biolegend	304108
APC Anti-Human CD38 antibody, for flow cytometry of human cord blood HSPCs	BD Biosciences	340439
PE Cy5 anti-human CD2 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555328
PE Cy5 anti-human CD3 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555341
PE Cy5 anti-human CD4 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555348
PE Cy5 anti-human CD7 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555362
PE Cy5 anti-human CD8 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555368
PE Cy5 anti-human CD11b antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555389
PE Cy5 anti-human CD14 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	562335
PE Cy5 anti-human CD16 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	561725
PE Cy5 anti-human CD19 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555414
PE Cy5 anti-human CD20 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555624
PE Cy5 anti-human CD56 antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	555517
PE Cy5 anti-human CD235A/GPA antibody, for flow cytometry of human cord blood hematopoietic cells (lineage cocktail)	BD Biosciences	559944
Alexa Fluor 647 anti-mouse CD144 antibody, for flow cytometry of mouse embryonic hematopoietic cells	BD Biosciences	562242
V450 anti-mouse CD45, for flow cytometry of mouse embryonic hematopoietic cells	BD Biosciences	560501
BV421 Anti-mouse CD48 antibody, for flow cytometry of mouse HSCs	Biolegend	103428
PE Anti-mouse Sca-1 antibody, for flow cytometry of mouse HSCs	Biolegend	108108
PE-Cy7 Anti-mouse CD150 antibody, for flow cytometry of mouse HSCs	Biolegend	115914
APC Anti-mouse c-Kit (CD117) antibody, for flow cytometry of mouse HSCs	Biolegend	313205
PE Anti-mouse GR-1/Ly-6G antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	108408
PE Anti-mouse Mac-1/CD11b antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	101208
PE-Cy7 Anti-mouse CD45 antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	103114
APC Anti-mouse CD4 antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	100516
APC Anti-mouse CD8a antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	100712
APC-Cy7 Anti-mouse B220/CD45R antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	103224
Brilliant Violet 421 anti-mouse CD41 antibody, for flow cytometry of mouse hematopoietic cells	Biolegend	133912
PE-Cy5 anti-mouse TER119 antibody, for flow cytometry of mouse hematopoietic cells	Thermo Fisher	15-5921-83
APC-eFluor 780 Streptavidin, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Thermo Fisher	47-4317-82
Biotin Anti-mouse Ter119 antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	116204
Biotin Anti-mouse CD4 antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	100508
Biotin Anti-mouse CD8a antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	100704
Biotin Anti-mouse CD127 (IL7R) antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	135006
Biotin Anti-mouse B220/CD45R antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	103204
Biotin Anti-mouse GR-1/Ly-6G antibody, for flow cytometry of mouse hematopoietic cells (lineage cocktail)	Biolegend	108404
Brilliant Violet 785 Anti-mouse CD45 antibody, for flow cytometry of mouse tissue myeloid cells	Biolegend	103149
Brilliant Violet 711 Anti-mouse/human CD11b antibody, for flow cytometry of mouse tissue myeloid cells	Biolegend	101242
Brilliant Violet 650 Anti-mouse F4/80 antibody, for flow cytometry of mouse tissue myeloid cells	Biolegend	123149
APC/Cyanine7 Anti-mouse CX3CR1 antibody, for flow cytometry of mouse tissue myeloid cells	Biolegend	149048
Brilliant Violet 421 Anti-mouse CD206 antibody, for flow cytometry of mouse tissue myeloid cells	Biolegend	141717
BD Horizon V450 Mouse anti-Human CD45 antibody, for flow cytometry of humanized mice	BD Biosciences	560367
APC-Cy7 anti-Human HLA-A/B/C antibody, for flow cytometry of humanized mice	Biolegend	311425
PE anti-Human CD33 antibody, for flow cytometry of humanized mice	Biolegend	303404
APC anti-Human CD19 antibody, for flow cytometry of humanized mice	Biolegend	302212
TruStain FcX anti-mouse CD16/32	Biolegend	101320
Anti-Rat and Anti-Hamster Ig κ Compensation Particles	BD Biosciences	552845
Anti-Mouse Ig κ Compensation Particles	BD Biosciences	552843
FcR Blocking Reagent, human	Miltenyi Biotec	130-059-901
Anti-mouse CD45 Microbeads, for magnetic enrichment	Miltenyi Biotec	130-052-301
Anti-APC Microbeads, for magnetic enrichment	Miltenyi Biotec	130-090-855
Goat anti-human SOX17 antibody, for immunostaining of human cells	R&D Systems	AF1924
Mouse anti-human CD144 antibody, for immunostaining of human cells	BD Biosciences	555661
Rabbit anti-human/mouse/rat RUNX1 antibody, for immunostaining of human cells	Abcam	92336
Mouse anti-human/mouse CD45 antibody, for immunostaining of human cells	eBioscience	14-0459082
Rabbit anti-human/mouse GFI1 antibody, for immunostaining of human cells	Cell Signaling Technology	31929
Rabbit anti-mouse RFP antibody, for immunostaining of mouse embryos	Rockland Immunochemicals	600-401-379
Rat anti-mouse KIT (CD117) antibody, for immunostaining of mouse embryos	Thermo Fisher	14-1171-82
Rat anti-mouse CD144 antibody, for immunostaining of mouse embryos	BD Biosciences	550548
Goat anti-mouse CD45 antibody, for immunostaining of mouse embryos	R&D Systems	AF114-SP
Donkey anti-goat Alexa Fluor 647 antibody	Thermo Fisher	A21447
Donkey anti-mouse Alexa Fluor 555 antibody	Thermo Fisher	A32773
Donkey anti-rabbit Alexa Fluor 647 antibody	Thermo Fisher	A31573
Donkey anti-rat Alexa Fluor 647 antibody	Thermo Fisher	A48268
Donkey anti-goat Alexa Fluor 555 antibody	Thermo Fisher	A21447
Chemicals, peptides and recombinant proteins
mTeSR Plus medium	STEMCELL Technologies	100-0276
Essential 8 medium	Thermo Fisher	A1517001
Penicillin/streptomycin	Thermo Fisher	15-140-122
KnockOut Serum Replacement	Thermo Fisher	10828028
Geltrex LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix	Thermo Fisher	A1413302
Recombinant Human Vitronectin Protein, Truncated (VTN-N)	Thermo Fisher	A14700
Versene solution	Thermo Fisher	15040066
TrypLE Express Enzyme (1X)	Thermo Fisher	12604013
Accutase (used in this study for in vitro cell dissociation)	Thermo Fisher	00-4555-56
Accutase (used in this study for brain tissue dissociation)	Innovative Cell Technologies	AT104
Type II Collagenase	Thermo Fisher	17101015
Liberase	Roche	5401119001
DNase I	Worthington	LS002007
HBSS without Ca2+/Mg2+	Thermo Fisher	14175103
HBSS with Ca2+/Mg2+	Thermo Fisher	24020117
Percoll	Cytiva	17-0891-02
Papain	Worthington Biochemical	LS003118
F062-mercaptoethanol (2-mercaptoethanol)	Thermo Fisher	21985023
Cysteine HCl	Sigma	C7477
M199 Media	Thermo Fisher	11150059
DMEM/F12 + GlutaMAX	Thermo Fisher	10565042
IMDM + GlutaMAX	Thermo Fisher	31980-097
F12 + GlutaMAX	Thermo Fisher	31765-092
αMEM + nucleosides	Thermo Fisher	12-571-063
Polyvinyl alcohol (PVA)	Sigma	P8136-250G
1-thioglycerol	Sigma	M6145-100ML
Chemically defined lipid concentrate	Thermo Fisher	11905-031
Recombinant human insulin	Sigma	11376497001
Human transferrin	Sigma	10652202001
DNase/RNase free water	Thermo Fisher	10977023
EDTA	Thermo Fisher	15575020
DMSO	Sigma Aldrich	D2650-100ML
Thiazovivin	Tocris	3845
Recombinant human VEGF	R&D Systems	293-VE-0500
Recombinant human FGF2	R&D Systems	233-FB-01M
Recombinant human BMP4	R&D Systems	314-BP-050
Recombinant human Activin A	R&D Systems	338-AC-500/CF
GDC-0941	Cellagen Technology	C4321-25
Forskolin	Tocris	1099
XAV939	Tocris	3748
Ascorbic acid-2-phosphate (AA2P)	Sigma	49752-10G
DMH1	Tocris	4126
SB505124	Tocris	3263
CHIR99201	Tocris	4423
TTNPB	Tocris	0761
DLL4-E12	Vincent Luca’s laboratory (Moffitt Cancer Center)	Luca et al.125
LIF	R&D Systems	7734-LF-025
OSM	R&D Systems	295-OM-010
SR1	Cellagen	C7710-5
UM171	ApexBio	A8950
UNC0638	Tocris	4343
UNC1999	Tocris	4904
EED226	Selleck Chemicals	S8496
GM-CSF	Peprotech	300-03
M-CSF	Peprotech	300-25
IL-3	Peprotech	200-03
IL-6	Peprotech	200-06
FLT3L	Peprotech	300-19
FLT3L	R&D Systems	308-FK
TPO	R&D Systems	288-TP-005/CF
TPO	Peprotech	300-18
SCF	Peprotech	300-07
SCF	R&D Systems	255-SC
IL-7	Peprotech	200-07
IL-15	Peprotech	200-15
G-CSF	Peprotech	300-23
Bovine serum albumin (BSA)	Sigma	A2153
Bovine serum albumin (BSA), Fraction V	Thermo Fisher	15260-037
Tween-20	Sigma	P9416
Insulin-Transferrin-Selenium-Ethanolamine (ITS-X)	Thermo Fisher	51500-056
Sytox Red Dead Cell Stain	Thermo Fisher	S34859
DAPI	Thermo Fisher	D1306
Propidium iodide (PI)	Biolegend	421301
Propidium iodide (PI)	Sigma	P4170
Donkey Serum	Millipore Sigma	D9663-10ML
Triton X-100	Millipore Sigma	T8787-50ML
Triton X-100	Sigma	X100-500ML
PBS, pH 7.4	Thermo Fisher	10010049
(Z)-4-Hydroxytamoxifen (4OHT), for lineage tracing	Millipore Sigma	H7904-25MG
(E/Z)-4-hydroxytamoxifen-d5, internal standard for mass spectrometry	Cayman Chemical	34232
Corn oil	Sigma	C8267-500ML
ACK (Ammonium-Chloride-Potassium) Lysing Buffer	Thermo Fisher	A1049201
Dextran from Leuconostoc spp., molecular weight 450,000-650,000	Sigma	31392-50G
32% paraformaldehyde solution	Fisher Scientific	50-980-495
Methanol	Fisher Scientific	A412-1
D-Sucrose	Fisher Scientific	BP220-212
AkaLumine HCl (otherwise known as TokeOni)	Tocris	6555
Ethanol, Absolute (200 Proof), Molecular Biology Grade	Fisher Scientific	BP2818100
Critical commercial assays
RNeasy Micro kit	Qiagen	74004
High-Capacity cDNA Reverse Transcription Kit	Applied Biosystems	4368814
SensiFAST SYBR Green Lo-ROX Kit	Thomas Scientific	BIO-94050
Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3	10x Genomics	1000075
Chromium Single Cell B Chip Kit, 48 reactions	10x Genomics	1000073
MACS LS column	Miltenyi Biotec	130-042-401
Fetal Bovine Serum (FBS), Premium Select	R&D Systems (formerly Atlanta Biologicals)	S11550
EDTA-coated Microtainer Blood Collection Tube	BD Biosciences	365974
O.C.T. Compound	Fisher Scientific	23-730-571
ProLong Gold Antifade Mountant	Thermo Fisher	P36930
MethoCult H4435 Enriched	STEMCELL Technologies	04435
StemSpan Erythroid Expansion Supplement	STEMCELL Technologies	02692
StemSpan Serum-Free Expansion Medium II (SFEM II)	STEMCELL Technologies	09655
StemPro-34 serum-free medium (SFM)	Thermo Fisher	10640-019
StemSpan T Cell Generation Kit	STEMCELL Technologies	09940
ImmunoCult Human CD3/CD28/CD2 T Cell Activator	STEMCELL Technologies	10970
Bioanalyzer High Sensitivity RNA Analysis	Agilent	5067-1513
Bioanalyzer High Sensitivity DNA Analysis	Agilent	5067-4626
KAPA Library Quantification Kit	Kapa Biosystems	KK4854
Illumina Nextera XT DNA Sample Preparation Kit	Illumina	FC-131-1096
Deposited data
Single-cell RNA-sequencing data of E8.5-E11 whole mouse embryos	Jay Shendure’s laboratory (University of Washington)	NCBI Accession: GSE186069 and NCBI Accession: GSE228590 (Qiu et al.85)
Single-cell RNA-sequencing data of hematopoietic progenitor and endothelial cells isolated from the E10-E11 mouse embryo dorsal aorta	Catherine Robin’s laboratory (Hubrecht Institute)	NCBI Accession: GSE112642 (Baron et al.28)
Single-cell RNA-sequencing data of whole E8.5 mouse embryos, accessible via online browser	John Marioni’s and Berthold Göttgens’s laboratories (University of Cambridge)	https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018/ (Pijuan Sala et al.81)
Bulk population RNA-sequencing data of FACS-purified CD144+ CD45+ HSCs and CD144- CD45+ non-HSCs from human fetal Carnegie Stage 15-16 (CS15-16) dorsal aorta	Alexander Medvinsky’s laboratory (University of Edinburgh)	NCBI Accession: GSE151877 (Crosse et al.143)
Single-cell RNA-sequencing profiles of human fetal 5- and 5.5-week-old aorta-gonad-mesenephros (AGM) cells	Hanna Mikkola’s laboratory (University of California Los Angeles)	NCBI Accession: GSE162950, samples GSM4968832 and GSM4968833 (Calvanese et al.30)
Single-cell RNA-sequencing profiles of hPSC-derived hematopoietic progenitors, differentiated using the Elefanty, Stanley, and Ng laboratories’ protocol30	Hanna Mikkola’s laboratory (University of California Los Angeles)	NCBI Accession: GSE162950, sample GSM6205033 (Calvanese et al.30)
Single-cell RNA-sequencing profiles of hPSC-derived hematopoietic progenitors, differentiated using the Keller laboratory’s protocol54	Ludovic Vallier’s, Daniel Ortmann’s, and Ana Cvejic’s laboratories (University of Cambridge)	European Bioinformatics Institute Accession: E-MTAB-8205, sample EXP2_CTRL2_4823STDY7231845 (Canu et al.144)
Single-cell RNA-sequencing profiles of hPSC-derived hematopoietic progenitors, differentiated using the Zandstra laboratory’s protocol145	Peter Zandstra’s laboratory (University of British Columbia)	NCBI Accession: GSE207157, sample GSM6280645 (Michaels et al.145)
Bulk-population RNA-sequencing timecourse profiling of hPSCs differentiating into HLF+ HOXA+ hematopoietic progenitors, differentiated using the present protocol	Kyle Loh’s and Lay Teng Ang’s laboratories (Stanford University)	NCBI Accession: PRJNA1074858 (this study)
Single-cell RNA-sequencing timecourse profiling of hPSCs differentiating into HLF+ HOXA+ hematopoietic progenitors, differentiated using the present protocol	Kyle Loh’s and Lay Teng Ang’s laboratories (Stanford University)	NCBI Accession: PRJNA1073685, also accessible via an interactive web browser: https://anglohlabs.shinyapps.io/blood_devcell_shiny/ (this study)
Experimental models: cell lines
H1 hESCs	WiCell	WiCell, WA01
H7 hESCs	WiCell	WiCell, WA07
H9 hESCs	WiCell	WiCell, WA09
H1 SOX17-2A-mPlum hESCs	Kyle Loh’s and Lay Teng Ang’s laboratories (Stanford University)	Ang et al.104
HES3 MIXL1-GFP hESCs	Andrew Elefanty’s, Edouard Stanley’s, and Elizabeth Ng’s laboratories (Murdoch Children’s Research Institute)	Davis et al.102
TkDA3-4 RUNX1-2A-mOrange hiPSCs	Hiromitsu Nakauchi’s laboratory (Stanford University)	Ikeda et al.126
iSU223n hiPSCs	Hiromitsu Nakauchi’s laboratory (Stanford University)	Nishimura et al.146
iLC13-F1 hiPSCs	Hiromitsu Nakauchi’s laboratory (Stanford University)	Ando et al.147
H7 CAG-AkaLuc-PuroR hESCs	Kyle Loh’s laboratory (Stanford University)	This study
WTC11 hiPSCs	Coriell Institute for Medical Research	Coriell Institute for Medical Research, GM25256, Kreitzer et al.148
OP9-DLL4-IRES-GFP feeder cells	Juan Carlos Zúñiga-Pflücker’s laboratory (University of Toronto)	Mohtashami et al.149
MS5 feeder cells	DSMZ	ACC 441
Human cord blood CD34+ hematopoietic stem and progenitor cells (pooled from mixed donors)	StemExpress	CB3400.5C
Experimental models: organisms/strains
Mus musculus (mouse): Cx40-CreERT2	Lucile Miquerol’s laboratory (Aix-Marseille Université)	Beyer et al.77
Mus musculus (mouse): Efnb2-CreERT2	Kyle Loh’s laboratory (Stanford University)	This study (being deposited at The Jackson Laboratory [JAX], 038831)
Mus musculus (mouse): Apj-CreERT2	Kristy Red-Horse’s laboratory (Stanford University)	Chen et al.91
Mus musculus (mouse): Rosa26-CAG-LoxP-Stop-LoxP-ZsGreen (Ai6)	The Jackson Laboratory	JAX 007906 (Madisen et al.78)
Mus musculus (mouse): FVB/NJ	The Jackson Laboratory	JAX 001800
Mus musculus (mouse): C57BL/6-CD45.2	The Jackson Laboratory	JAX 000664
Mus musculus (mouse): C57BL/6-CD45.1 (Pepboy)	The Jackson Laboratory	JAX 002014
Mus musculus (mouse): NOD-SCID Il2rg-/- (NSG)	The Jackson Laboratory	JAX 005557 (Shultz et al.150)
Oligonucleotides
Primers	See Table S4	N/A
HCR3 probe for mouse Gja5 (Cx40), compatible with amplifier B3	Molecular Instruments	Custom probe against Gja5 (sequence deposited at NCBI accession NM_001271628)
HCR3 probe for CreERT2, compatible with amplifier B1	Molecular Instruments	Custom probe against CreERT2 (sequence deposited at https://www.addgene.org/14797/)
HCR3 B3-Alexa Fluor 647 amplifier probe	Molecular Instruments	B3-Alexa Fluor 647
HCR3 B1-Alexa Fluor 488 amplifier probe	Molecular Instruments	B1-Alexa Fluor 488
Software and algorithms
anndata	Fabian Theis’s laboratory (Helmholtz Munich)	https://github.com/theislab/anndata
AnnotationDbi	Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li (Bioconductor Team)	https://github.com/Bioconductor/AnnotationDbi
biomaRt	Damian Smedley, Syed Haider, Benoit Ballester, Richard Holland, Darin London, Gudmundur Thorisson, Arek Kasprzyk (Bioconductor Team)	https://github.com/grimbough/biomaRt
CellRanger	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
DESeq2	Michael Love’s laboratory (University of North Carolina at Chapel Hill)	https://github.com/thelovelab/DESeq2 (Love et al.151)
dplyr	Hadley Wickham (Tidyverse Team)	https://github.com/tidyverse/dplyr
ggplot2	Hadley Wickham (Tidyverse Team)	https://github.com/tidyverse/ggplot2
hdf5r	Holger Hoefling and Mario Annau (Novartis Institutes for BioMedical Research)	https://github.com/hhoeflin/hdf5r/
FIJI/ImageJ	Albert Cardona’s laboratory (University of Cambridge)	https://imagej.net/software/fiji/ (Schindelin et al.152)
Kallisto	Lior Pachter’s laboratory (California Institute of Technology)	https://pachterlab.github.io/kallisto/ (Bray et al.153)
matrix	Timothy Davis’s laboratory (Texas A&M University)	https://Matrix.R-forge.R-project.org
org.Hs.eg.db	Martin Mächler (ETH Zürich)	http://bioconductor.org/packages/org.Hs.eg.db/
patchwork	Thomas Lin Pederson (Unaffiliated)	https://github.com/thomasp85/patchwork
RColorBrewer	Erich Neuwirth (University of Vienna)	http://colorbrewer2.org
RCurl	CRAN Team	https://curl.se/libcurl/
reticulate	Yuan Tang (Reticulate Team)	https://github.com/rstudio/reticulate
rhdf5	Bernd Fischer, Mike Smith, Gregoire Pau, Martin Morgan, Daniel van Twisk (European Molecular Biology Laboratory)	https://github.com/grimbough/rhdf5
RStudio v 2022.12.0+353	RStudio Team	https://www.rstudio.com/
scanpy	Fabian Theis’s laboratory (Helmholtz Munich)	https://github.com/theislab/Scanpy
scCustomize	Samuel Marsh (Children's Hospital Boston)	https://github.com/samuel-marsh/scCustomize
Seurat v4.3.0	Rahul Satija’s laboratory (New York Genome Center)	https://github.com/satijalab/seurat (Hao et al.154)
SeuratDisk	Rahul Satija’s laboratory (New York Genome Center)	https://github.com/mojaveazure/seurat-disk
tidyverse	Hadley Wickham (Tidyverse Team)	https://github.com/tidyverse
tximport	Michael Love’s laboratory (University of North Carolina at Chapel Hill)	https://bioconductor.org/packages/release/bioc/html/tximport.html (Soneson et al.155)
viridis	Simon Garnier, Noam Ross, Robert Rudis, Pedro Camargo, Marco Sciaini, Cédric Sherer (New Jersey Institute of Technology)	https://github.com/sjmgarnier/viridis
Computational scripts used for genomics analyses in this study	Kyle Loh’s laboratory (Stanford University)	https://github.com/lohlaboratory/blood-differentiation (https://doi.org/10.5281/zenodo.10729568)