REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-mouse CD4-PerCP-Cy5.5 (clone: RM4-5)	TONBO biosciences	Cat# 65-0042-U100; RRID: AB_2621876
Anti-mouse CD8a-PerCP-Cy5.5 (clone: 53-6.7)	TONBO biosciences	Cat# 65-0081-U100; RRID: AB_2621882
Anti-mouse B220-PerCP-Cy5.5 (clone: RA3-6B2)	TONBO biosciences	Cat# 65-0452-U100; RRID: AB_2621892
Anti-mouse B220-APC (clone: RA3-6B2)	BioLegend	Cat# 103212; RRID: AB_312997
Anti-mouse Ter-119-PerCP-Cy5.5 (clone: TER-119)	TONBO biosciences	Cat# 65-5921-U100
Anti-mouse Gr1 (Ly-6G/6C)-PerCP-Cy5.5 (clone: RB6-8C5)	BioLegend	Cat# 108428; RRID: AB_893558
Anti-mouse Gr1-PE-Cy7 (clone: RB6-8C5)	TONBO biosciences	Cat# 60-5931-U100; RRID: AB_2621870
Anti-mouse Mac1 (CD11b)-PerCP-Cy5.5 (clone: M1/70)	TONBO biosciences	Cat# 65-0112-U100; RRID: AB_2621885
Anti-mouse Mac1-PE-Cy7 (clone: M1/70)	TONBO biosciences	Cat# 60-0112-U100; RRID: AB_2621836
Anti-mouse CD45.1-PE (clone: A20)	BD biosciences	Cat# 553776; RRID: AB_395044
Anti-mouse CD45.2-BV421 (clone: 104)	BD biosciences	Cat# 562895; RRID: AB_2737873
Anti-mouse CD45.2-Alexa Four 700 (clone: 104)	BioLegend	Cat# 109822; RRID: AB_493731
Anti-mouse Sca-1 (Ly-6A/E)-PE-Cy7 (clone: E13-161.7)	BioLegend	Cat# 122514; RRID: AB_756199
Anti-mouse Sca-1-Alexa488 (clone: E13-161.7)	BioLegend	Cat# 122516; RRID: AB_756201
Anti-mouse Sca-1-BV785 (clone: D7)	BioLegend	Cat# 108139; RRID AB_2565957
Anti-mouse c-Kit (CD117)-APC-Cy7 (clone: 2B8)	BioLegend	Cat# 105826; RRID: AB_1626278
CD117 MicroBeads Mouse	Miltenyi Biotec	Cat# 130-091-224
Anti-mouse CD150-PE (clone: TC15-12F12.2)	BioLegend	Cat# 115904; RRID: AB_313683
Anti-mouse CD150-BV421 (clone: TC15-12F12.2)	BioLegend	Cat# 115926; RRID: AB_2562190
Anti-mouse CD150-BV785 (clone: TC15-12F12.2)	BioLegend	Cat# 115937; RRID: AB_2565962
Anti-mouse CD48-FITC (clone: HM48-1)	BioLegend	Cat# 103404; RRID: AB_313019
Anti-mouse CD48-PE (clone: HM48-1)	BioLegend	Cat# 103406; RRID: AB_313021
Anti-mouse CD48-APC (clone: HM48-1)	BioLegend	Cat# 103412; RRID: AB_571997
Anti-mouse CD48-BV510 (clone: HM48-1)	BD biosciences	Cat# 563536; RRID: AB_2738266
Anti-mouse CD48-Biotin (clone: HM48-1)	BioLegend	Cat# 103410; RRID: AB_528827
Fc-block (anti-mouse CD16/32) (clone: 2.4-G2)	BD biosciences	Cat# 553142; RRID: AB_394657
Anti-mouse CD16/32-BV510 (clone: 2.4G2)	BD biosciences	Cat# 740111; RRID: AB_2739869
Anti-mouse CD16/32- PE (clone: 93)	BioLegend	Cat# 101307; RRID: AB_312807
Anti-mouse CD16/32- Alexa700 (clone: A93)	Thermo Fisher Scientific	Cat# 56-4321-80; RRID: AB_493994
Anti-mouse CD34-FITC (clone: RAM34)	BD biosciences	Cat# 562608; RRID: AB_11154576
Anti-mouse CD34-BV421 (clone: MEC14.7)	BioLegend	Cat# 119321; RRID: AB_10900980
Anti-mouse Flt3 (CD135)-APC (clone: A2F10)	BioLegend	Cat# 135310; RRID: AB_2107050
Anti-mouse CD201 (EPCR)-PE (clone: RCR-16)	BioLegend	Cat# 141504; RRID: AB_10895909
Anti-mouse CD45-FITC (clone: 30-F11)	BD biosciences	Cat# 553080; RRID: AB_394609
Anti-mouse CD45-PE (clone: 30-F11)	BioLegend	Cat# 103134; RRID: AB_2562559
Anti-mouse CD45-BV421 (clone: 30-F11)	BioLegend	Cat# 103134; RRID: AB_2562559
Anti-mouse CD45-BV786 (clone: 30-F11)	BD biosciences	Cat# 564225; RRID: AB_2716861
Anti-mouse CD45-Biotin (clone: 30-F11)	BioLegend	Cat# 103104; RRID: AB_312969
Anti-Streptavidin-Alexa Fluor 555 (clone: TER-119)	Thermo Fisher Scientific	Cat# S21381; RRID: AB_2307336
CD34 MicroBeads Human	Miltenyi Biotec	Cat# 130-046-702
Anti-human CD34-FITC (clone: 581)	BD Bioscience	Cat# 560942; RRID: AB_396150
Anti-human CD34-APC (clone: 561)	BioLegend	Cat# 343607; RRID: AB_2074356
Anti-human CD38-PerCP-Cy5.5 (clone: HIT2)	BD Bioscience	Cat# 551400; RRID: AB_394184
Anti-human CD45RA-PE (clone: HI100)	BD Bioscience	Cat# 555489; RRID: AB_395880
Anti-human CD90-PE-Cy7 (clone: 5E10)	BioLengend	Cat# 328123; RRID: AB_2561692
Anti-human CD201 (EPCR)-BV421 (clone: RCR-252)	BD Bioscience	Cat# 743552; RRID: AB_2741576
Anti-human CD201 (EPCR)-PE (clone: RCR-401)	BioLegend	Cat# 351903; RRID: AB_10897801
Anti-human CD45-PE (clone: 2D1)	BioLegend	Cat # 368510; RRID: AB_2566370
Anti-mouse Ki67-eFlour660 (clone: SolA15)	eBioscience	Cat# 50-5698-82; RRID: AB_2574235
Anti-mouse/human Ki67-FITC (clone: 11F6)	BioLegend	Cat# 151212; RRID: AB_2814055
Annexin V-APC	BioLegend	Cat# 640920; RRID: AB_2561515
Chemicals, peptides, and recombinant proteins
PBS	Nacalai Tesque	Cat# 14249-24
SF-O3	SEKISUI MEDICAL	SS1303
DMEM/Ham’s-F12 medium	Nacalai Tesque	Cat# 11581-15
RPMI1640	Nacalai Tesque	Cat# 30263-95
StemSpan SFEM	STEMCELL Technologies	Cat# 09650
HemEX-Type9A	Cell Science & Technology Institute	Cat# A5P00P01C
MethoCult GF M3434	STEMCELL Technologies	Cat# 03444
MethoCult H4434	STEMCELL Technologies	Cat# 04434
Insulin-Transferrin-Selenium-Ethanolamine (ISTX) 1000x	Thermo Fisher Scientific	Cat# 51500-056
2-mercapto ethanol (2-ME) 1000x	Thermo Fisher Scientific	Cat# 21985-023
Penicillin	Meiji Seika	PGLD755
Streptomycin sulfate	Meiji Seika	SSDN1013
Fetal bovine serum	Thermo Fisher Scientific	Cat# 10270-106
Bovine serum albumin	Sigma Aldrich	Cat# A4503-100G
Palmitic acid	Wako Pure Chemical Corporation	Cat# 165-00102
Oleic acid	Sigma Aldrich	Cat# O1383-1G
Cholesterol	Sigma Aldrich	Cat# C3045-5G
Sodium Hydroxide	Wako Pure Chemical Corporation	Cat# 191-01665
Recombinant Murine SCF	PeproTech	Cat# 250-03
Recombinant Human TPO	PeproTech	Cat# 300-18
Recombinant Murine G-CSF	PeproTech	Cat# 250-05
Recombinant Human SCF	PeproTech	Cat# 250-31L
Recombinant Human FLT3L	PeproTech	Cat# 300-19
Recombinant Human IL-3	PeproTech	Cat# 200-03
Recombinant Human IL-6	PeproTech	Cat# 200-06
DMSO	Sigma Aldrich	Cat# D8418
UM171	Selleck	Cat# 7608
Lymphoprep	STEMCELL Technologies	Cat# 07811
BD Cytofix/Cytoperm Fixation/Permeabilization Solution Kit	Thermo Fisher Scientific	Cat# BDB554714
5-ethynyl-2′-deoxyuridine (EdU)	Tokyo Chemical industry	Cat# E1057
Tris-hydroxypropyltriazolymethylamine (THPTA)	Click Chemistry Tools	Cat# 1010
AFDye 647 Picolyl Azide	Click Chemistry Tools	Cat# 1300-1
Copper (Brenet et al.)75 Sulfate Pentahydrate	Tokyo Chemical Industry Co., Ltd.	Cat# 7758-99-8
Ascorbic acid	Tokyo Chemical Industry Co., Ltd.	Cat# 03428-72
Click-iT Plus EdU Alexa Flour 647 Flow Cytometry Assay Kit	Thermo Fisher Scientific	Cat# C10634
Propidium iodide	Lifetechnologies	Cat# P3566
Hoechst 33342	Thermo Fisher Scientific	Cat# H3570
TrueCut Cas9 Protein v2	Thermo Fisher Scientific	Cat# A36299
Flow-Check Fluorospheres	Beckman Coulter	Cat# 7547053
SuperSignal West Femto Maximum Sensitivity Substrate	Thermo Fisher Scientific	Cat# 34094
Critical commercial assays
Neon Transfection System 10μL Kit	Thermo Fisher Scientific	Cat# MPK1096
CUGA7 sgRNA Synthesis Kit	Nippon Gene	Cat# 314-08691
TaKaRa Ex Taq	Takara Bio Inc	Cat# RR001A
Q5 High-Fidelity 2x Master Mix	New England BioLabs	Cat# M0492S
NucleoSpin Tissue XS	Macherey Nagel	Cat# 740901.50
Wizard SV Gel and PCR Clean-Up System	Promega	Cat# A9282
Annexin V-PE Apoptosis Detection Kit	BD Biosciences	Cat# 559763
RNeasy Mini Kit	QIAGEN	Cat# 74136
SuperScript VILO cDNA Synthesis Kit	Thermo Fisher Scientific	Cat# 11754050
TB Green Premix Ex Taq II	Takara Bio	Cat# RR820D
AAVpro Purification Kit	Takara Bio	Cat# 6666
AAV Helper Free Expression System	Cell Biolabs., Inc	Cat# VPK-402
Deposited data
RNA-seq	This paper	DNA Data Bank of Japan (DDBJ): Accession #DRA014998
Experimental models: Organisms/strains
Mouse: C57BL/6JJmsSlc	Japan SLC, Inc.	http://www.jslc.co.jp/english/index2.htm
Mouse: C57BL/6J-Ly5.1	CLEA Japan, Inc	N/A
Mouse: C57BL/6-Tg(Ubc-GFP)30Scha/J	The Jackson Laboratory	JAX stock #004353
Mouse: Evi1-IRES-GFP mice	Kataoka et al.70	N/A
Oligonucleotides
sgRNA Common primer: AAAAGCACCGACTCGGTGCC	This paper	N/A
sgRNA Reversed primer: AAAAGCACCGACTCGGTGCCA CTTTTTCAAGTTGATAACGGAC TAGCCTTATTTTAACTTGCT ATT TCTAGCTCTAAAAC	This paper	N/A
Rosa sgRNA target Forward primer: ttaatacgactcactataggACTCCAGTCT TTCTAGAAGAgttttagagctagaaatagc	Chu et al.60	N/A
Mouse CD45 sgRNA target Forward primer: ttaatacgactcactataGGGTTTGTGGCTCAAA CTTCgttttagagctagaaatagc	This paper	N/A
GFP sgRNA target Forward primer: ttaatacgactcactataGGGCGAGGAGCTGTT CACCGgttttagagctagaaatagc	Gundry et al.35
Rosa forward primer: CCAAAGTCGCTCTGAGTTGTTATCAGT	This paper	N/A
Rosa reverse primer: GGAGCGGGAGAAATGGATATGAAG	This paper	N/A
Rosa sequence primer: ACATAGTCTAACTCGCGACAC	This paper	N/A
Mouse CD45 forward primer: AGAAGCCATTGCACTGACTTTG	This paper	N/A
Mouse CD45 reverse primer: GTGTGATCTTTCCCCGAAACAT	This paper	N/A
Mouse CD45 sequence primer: CTGCAAAGAGGACCCTTTACAGT	This paper	N/A
Ubc-GFP forward primer: GTTCACCTTGATGCCGTTCT	This paper	N/A
Ubc-GFP reverse and sequence primer: CACCCGTTCTGTTGGCTTAT	This paper	N/A
Rosa sgRNA: ACUCCAGUCUUUCUAG AAGA	Synthego Chu et al.60	N/A
Mouse CD45 sgRNA: GGGUUUGUGGCU CAAACUUC	Synthego	N/A
AAVS1 sgRNA: GGGGCCACUAGGGA CAGGAU	Synthego Bak et al.37	N/A
Human CD45 sgRNA: GGUGCUGGUGUUGGGCGCAC	Synthego Gundry et al.35	N/A
GFP sgRNA: GGGCGAGGAGCU GUUCACCG	Synthego Gundry et al.35	N/A
Alt-R CRISPR-Cas9 crRNA XT for CD45: GGGTTTGTGGCTCAAACTTC	IDT	N/A
Alt-R CRISPR-Cas9 tracRNA	IDT	N/A
Alt-R CRISPR-Cas9 tracRNA ATTO	IDT	N/A
AAV LHA in-out forward primer (Rosa genome): CTCTGGGGGAGTCGTTTTACC	This paper	N/A
AAV LHA in-out reverse primer (CAG promoter): CCAGGCGGGCCATTTACC	This paper	N/A
AAV RHA in-out forward primer (EGFP): AACGA GAAGCGCGATCACAT	This paper	N/A
AAV RHA in-out reverse primer (Rosa genome): ACAGCCTCGATTTGTGGTGT	This paper	N/A
AAV titration qPCR forward primer: GGAACCCCTAGTGATGGAGTT	Aurnhammer et al.83	N/A
AAV titration qPCR reverse primer: CGGCCTCAGTGAGCGA	Aurnhammer et al.83	N/A
Infb1 qPCR forward primer: CCTGGAGCAGCTGAATGGAA	Takara Bio	N/A
Infb1 qPCR reverse primer: TGGATGGCAAAGGCAGTGAA	Takara Bio	N/A
Oas2 qPCR forward primer: GGCCTGGTACAGCCTTGGAA	Takara Bio	N/A
Oas2 qPCR reverse primer: AGTCTTTGCCAGATCACTCCAGAA	Takara Bio	N/A
Ddx58 (RIG-I) qPCR forward primer: AGCCAAGGATGTCTCCGAGGAA	Liu et al.84	N/A
Ddx58 (RIG-I) qPCR reverse primer: ACACTGAGCACGCTTTGTGGAC	Liu et al.84	N/A
Isg15 qPCR forward primer: CATCCTGGTGAGGAACGAAAGG	Liu et al.84	N/A
Isg15 qPCR reverse primer: CTCAGCCAGAACTGGTCTTCGT	Liu et al.84	N/A
β-actin qPCR forward primer: CATCCGTAAAGACCTCTATGCCAAC	Takara Bio	N/A
β-actin qPCR reverse primer: ATGGAGCCACCGATCCACA	Takara Bio	N/A
Software and algorithms
FlowJo version 10.7.2	Tree Star	https://www.flowjo.com/solutions/flowjo
SnapGene	GLS Biotech	https://www.snapgene.com/
Molecular Biology tool	Benchling	https://www.benchling.com
TIDE	Brinkman et al.85	https://tide.nki.nl
Prism v7	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
Imaris 9.8.2	Oxford Instruments	https://imaris.oxinst.com/support/imaris-release-notes/9-8-0
ImageJ	National Institutes of Health	https://imagej.nih.gov/ij/
R v.4.1.0	R Development Core Team (2008)	http://www.r-project.org
DESeq2	Love et al.86	http://bioconductor.org/packages/release/bioc/html/DESeq2.html
fGSEA	Korotkevich et al.87	http://bioconductor.org/packages/release/bioc/html/fgsea.html
GSVA	Hanzelmann et al.88	http://bioconductor.org/packages/release/bioc/html/GSVA.html
Others
Neon Transfection System	Thermo Fisher Scientific	Cat# MPK5000
Neon Transfection System 10μL Kit	Thermo Fisher Scientific	Cat# MPK1096
Nucleofector 2b	Lonza	AAB-1001
Human CD34+ Cell Nucleofector Kit	Lonza	PVA-1003
NanoDrop Onec Microvolume UV-Vis Spectrophotometer	Thermo Fisher Scientific	Cat# ND-ONEC-W
Hiseq1500	Illumina