REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-HA tag (Abcam)	Sigma	Cat# H6908; RRID: AB_260070
Anti-Histone H3 (Rabbit polyclonal)	Abcam	Cat# ab1791; RRID: AB_302613
Anti-Histone H3K27ac	Abcam	Cat# ab4729; RRID: AB_2118291
Anti-Histone H3K4me3	Merk	Cat# 07-473; RRID: AB_1977252
Anti-human AML1 (Rabbit Polyclonal)	Cell Signaling Technology	Cat# 4334; RRID: AB_2184099
Anti-LDB1	Abcam	Cat# ab96799; RRID: AB_10679400
Anti-LMO2	R&D Systems	Cat# AF2726; RRID: AB_2249968
Anti-RUNX1	Abcam	Cat# ab23980; RRID: AB_2184205
APC anti-human CD38	BD PharMingen	Cat# 555462; RRID: AB_398599
APC anti-human CD90	BD PharMingen	Cat# 559869; RRID: AB_398677
BV-421 anti-human CD326 (EpCam)	BioLegend	Cat# 324220; RRID: AB_2563847
BV-421 anti-human CD34	BioLegend	Cat# 343609; RRID: AB_11147951
BV-421 anti-human CD45	BioLegend	Cat# 304032; RRID: AB_2561357
BV-421 anti-human CD90	BioLegend	Cat# 328121; RRID: AB_10933261
DyLight® 650-conjugated anti-HA tag [16B12]	Abcam	Cat# ab117515; RRID: AB_10999718
FITC-conjugated BrdU and IgG	BD PharMingen	Cat# 556028; RRID: AB_396304
PE anti-human CD9	BD PharMingen	Cat# 555372; RRID: AB_395774
PeCy7 anti-human CD16	BioLegend	Cat# 302015; RRID: AB_314215
PeCy7 anti-human CD34	BioLegend	Cat# 343516; RRID: AB_1877251
Bacterial and Virus Strains
One Shot™ TOP10 Chemically Competent E. Coli	Thermo Fisher Scientific	Cat# C404010
Chemicals, Peptides, and Recombinant Proteins
2-Mercaptoethanol	Thermo Fisher Scientific	Cat# 21985-023
a- Monothioglycerol (MTG)	Merck	Cat# M6145
Accutase solution	Merk	Cat# A6964
Activin A (ACT)	R&D Systems	Cat# 338-AC
Albumin from rice endosperm	ScienCell Research Labs	Cat# OsSA
AMPure magnetic beads	Beckman Coulter	Cat# A63881
Ascorbic acid 2-phosphate (AA2P)	Merck	Cat# A8960
Bone morphogenetic protein 4 (BMP4)	R&D Systems	Cat# 314-BP
Bovostar acid-stripped Bovine Serum Albumin (BSA)	Bovogen	Cat# BSAS 0.1
BrdU	Sigma	Cat# B5002
CHIR99021	Tocris Biosciences	Cat# 4423
Collagenase Type 4	Worthington	Cat# CLS-4
Digitonin	Promega	Cat# G9441
Dimethyl sulfoxide Hybri-MaxTM (DMSO)	Merk	Cat# D2650
DMEM Nutrient Mixture F- 12 1x + L-glutamine Na bicarbonate (DMEM/F12)	Thermo Fisher Scientific	Cat# 11320-033
Erythropoietin (EPO)	PeproTech	Cat# 100-64
Fibroblast Growth Factor (FGF2)	PeproTech	Cat# 100-18B
Fixation/Permeabilization solution	BD PharMingen	Cat# 554722
FMS-like tyrosine kinase 3 receptor (FLT3) ligand	PeproTech	Cat# 300-19
GlutaMAXI100x	Thermo Fisher Scientific	Cat# 35050-061
Ham’s F12	Thermo Fisher Scientific	Cat# 11765-062
Human low-density lipoproteins (hLDL)	Stem Cell Technologies	Cat# 02698
Insulin-like growth factor 2 (IGF2)	PeproTech	Cat# 100-12
Insulin-Transferrin-Selenium-E (ITS-E)	In Vitria	Cat# 777ITS092
Interleukin 3 (IL-3)	PeproTech	Cat# 200-03
Interleukin 6 (IL-6)	PeproTech	Cat# 200-06
Iscove’s Modified Dulbecco’s Media (IMDM) with no phenol red	Themo Fisher Scientific	Cat# 21056-023
KnockOut Serum Replacer (KO-SR)	Thermo Fisher Scientific	Cat# 10828028
L-Ascorbic acid	Merck	Cat# A4403
Linoleic acid	Merck	Cat# L2376
Linolenic acid	Merck	Cat# L1376
Matrigel Growth Factor Reduced phenol red-free	In Vitro Technologies	Cat# FAL356231
Methanol-free Formaldehyde	Thermo Fisher Scientific	Cat# 28906
MethoCult™ H4100	Stem Cell Technologies	Cat# 01400
NEBNext High-Fidelity 2x PCR Master Mix	New England Biolabs	Cat# M0541
NextSeq® 500/550 High Output 150 cycle sequencing kit v2	Illumina	Cat# FC-404-2002
NextSeq® 500/550 High Output 75 cycle sequencing kit v2	Illumina	Cat# FC-404-2005
Non-essential amino acids (NEAA) 100X	Thermo Fisher Scientific	Cat# 11140-050
Penicillin/Streptomycin (Pen/Strep)	Thermo Fisher Scientific	Cat# 15140122
Perm/Wash buffer	BD PharMingen	Cat# 554723
Polyvinyl alcohol (PVA)	Merck	Cat# P8136
Protein Free Hybridoma Medium II (PFHMII)	Thermo Fisher Scientific	Cat# 12040077
SB431542	Sapphire Bioscience	Cat# 13031
Soybean Oil (lecithin)	Merck	Cat# S7381
Stem cell factor (SCF)	PeproTech	Cat# 300-07
SuperScript II Reverse Transcriptase	Thermo Fisher Scientific	Cat# 18064022
SyntheChol	Merck	Cat# S5442
Thrombopoietin (TPO)	PeproTech	Cat# 300-18
TrypLE™ Select Enzyme	Thermo Fisher Scientific	Cat# 12563011
Vascular endothelial growth factor (VEGF)	PeproTech	Cat# 100-20
Vybrant DyeCycle Violet Stain	Thermo Fisher Scientific	Cat# V35003
Critical Commercial Assays
Bioline Isolate II RNA Mini Kit	Bioline	Cat# BIO-52072
CD34 UltraPure human MicroBeads Kit	Miltenyi Biotec	Cat# 130-100-453
Chromium Single Cell 3′ Library and Gel Bead Kit v2	10X Genomics	Cat# PN-120237
High Sensitivity DNA Chip	Agilent Technologies	Cat# 5067-4626
KAPA Hyper Prep Kit	Roche	Cat# KR0961
KAPA Library Quantification Kit Illumina Sequencing Platforms	Roche	Cat# KR0405
MACS Starting Kit	Miltenyi Biotec	Cat# 130-091-632
MinElute Reaction Cleanup Kit	QIAGEN	Cat# 28204
Nextera DNA Library Prep Kit	Illumina	Cat# FC-121-1030
Pierce BCA Protein Assay Kit	Thermo Fisher Scientific	Cat# 23225
SuperSignal PICO reagent mix	Thermo Fisher Scientific	Cat# 34579
Tetro cDNA synthesis kit	Bioline	Cat# BIO-65042
TruSeq® Stranded mRNA Library Prep	Illumina	Cat# 20020594
Universal Magnetic Co-IP Kit	Active Motif	Cat# 54002
Deposited Data
Bulk RNA-seq data	This study	GEO: GSE137673
ChIP-seq data	This study	GEO: GSE137673
ATAC-seq data	This study	GEO: GSE137673
scRNA-seq data	This study	GEO: GSE137673
Experimental Models: Cell Lines
SOX17mCHERRY/wRUNX1CGFP/w hESC H9 line	Ng et al., 2016	N/A
Inducible RUNX1-ETO SOX17mCHERRY/wRUNX1CGFP/w hESC H9 line	This paper	N/A
Oligonucleotides
Oligonucleotide sequences, see Table S1	This paper	N/A
GAPDH (TaqMan assay)	Thermo Fisher Scientific	RRID: Hs99999905_m1
GATA1 (TaqMan assay)	Thermo Fisher Scientific	RRID: HS00231112_m1
GFI1 (TaqMan assay)	Thermo Fisher Scientific	RRID: Hs00382207_m1
GFI1B (TaqMan assay)	Thermo Fisher Scientific	RRID: Hs01062469_m1
SPI1 (PU.1) (TaqMan assay)	Thermo Fisher Scientific	RRID: HS00231368_m1
RUNX1 COMMON (TaqMan assay)	Thermo Fisher Scientific	RRID: HS00231079_m1
RUNX1C (TaqMan assay)	Thermo Fisher Scientific	RRID: Hs01021967_m1
RUNX1T1 (TaqMan assay)	Thermo Fisher Scientific	RRID: Hs00231702_m1
Recombinant DNA
pSIEW-RUNX1-ETO	Bomken et al., 2013	N/A
pTREG-CAGGS-Tet3G-AAVS1	Qian et al., 2014	N/A
Software and Algorithms
Trimmomatic v0.32	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
Bowtie2 v2.2.6	Langmead and Salzberg., 2012	http://bowtie-bio.sourceforge.net/index.shtml
MACS2 v2.1.1	Zhang et al., 2008	https://github.com/taoliu/MACS
Picard v2.10.5	http://broadinstitute.github.io/picard	N/A
Homer v4.9.1	Heinz et al., 2010	http://homer.ucsd.edu/homer/
R v3.5.1	https://www.R-project.org/	N/A
Java TreeView v1.1	Saldanha, 2004	http://jtreeview.sourceforge.net/
deepTools v3.2.0	Ramírez et al., 2016	https://github.com/deeptools/deepTools
Hisat2 v2.1.0	Kim et al., 2015	https://daehwankimlab.github.io/hisat2/
Stringtie v1.3.3	Pertea et al., 2015	https://ccb.jhu.edu/software/stringtie/
Limma v3.26.9	Ritchie et al., 2015	https://bioconductor.org/packages/release/bioc/html/limma.html
Cytoscape v3.6.1	Shannon et al., 2003	https://cytoscape.org/
ClueGO v2.5.0	Bindea et al., 2009	http://apps.cytoscape.org/apps/cluego
dynamicTreeCut v1.63	Langfelder et al., 2008	https://cran.r-project.org/web/packages/dynamicTreeCut/index.html
GSEA v2.2.4	Subramanian et al., 2005	https://www.gsea-msigdb.org/gsea/index.jsp
CellRanger v2.1.1	https://www.10xgenomics.com/	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat v2.3.4	Butler et al., 2018	https://satijalab.org/seurat/
Monocle v2.10.1	Qiu et al., 2017, Trapnell et al., 2014	http://cole-trapnell-lab.github.io/monocle-release/
Other
Low attachment 96-well plates (Sterile)	Costar	Cat# COR3788
Ultra-low attachment 24-well plates	In Vitro AS	Cat# NUN144530
4-20% gradient polyacrylamide gel	Biorad	Cat# 456-8093
AML patient RNA-seq data	Assi et al., 2019	GEO: GSE108316
Hematopoietic progenitor RNA-seq data	Corces et al., 2016	GEO: GSE74912