REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
BD Pharm Lyse	BD Biosciences	Cat#555899; RRID: AB_2869057
Biotin anti-mouse CD45 Antibody	Biolegend	Cat#103104; RRID: AB_312969
Biotin anti-mouse CD71 Antibody	Biolegend	Cat#113803; RRID: AB_313564
CD41-Biotin	Biolegend	Cat#133930; RRID: AB_2572133
Lineage Cell Depletion Kit, mouse	Miltenyi Biotec	Cat#130-090-858
APC/Cyanine7 anti-mouse CD41 Antibody	Biolegend	Cat#133928; RRID: AB_2572131
APC/Cyanine7 anti-mouse CD3 Antibody	Biolegend	Cat#100222; RRID: AB_2242784
APC/Cyanine7 anti-mouse/human CD11b Antibody	Biolegend	Cat#101226; RRID: AB_830642
APC/Cyanine7 anti-mouse Ly-6G/Ly-6C (Gr-1) Antibody	Biolegend	Cat#108424; RRID: AB_2137485
APC/Cyanine7 anti-mouse TER-119/Erythroid Cells Antibody	Biolegend	Cat#116223; RRID: AB_2137788
APC/Cyanine7 anti-mouse/human CD45R/B220 Antibody	Biolegend	Cat#103224; RRID: AB_313007
APC/Cyanine7 anti-mouse CD45.1 Antibody	Biolegend	Cat#110716; RRID: AB_313505
APC/Cyanine7 anti-mouse CD45.2 Antibody	Biolegend	Cat#109824; RRID: AB_830789
PerCP/Cy5.5 anti-mouse Ly-6A/E (Sca-1)	Sony Biotechnologies	Cat#1212615; RRID: AB_2877117
APC anti-mouse CD31 Antibody	Biolegend	Cat#102410; RRID: AB_312905
PE anti-mouse CD51 Antibody	Biolegend	Cat#104106; RRID: AB_2129493
Hoechst Solution 33342	BD Biosciences	Cat#561908
Pacific Blue anti-mouse CD45 Antibody	Biolegend	Cat#103125; RRID: AB_493536
CD11b Monoclonal Antibody (M1/70), eFluor 450	ThermoFisher	Cat#48-0112-80; RRID: AB_1582237
PE/Cy7 anti-mouse CD140a Antibody	Biolegend	Cat#135911; RRID: AB_2715973
APC CD140b (PDGFRB) Monoclonal Antibody (APB5)	ThermoFisher	Cat#14-1402-82; RRID: AB_467493
PE anti-mouse CD106 Antibody	Biolegend	Cat#105713; RRID: AB_1134166
FITC CD107a antibody	BD Biosciences	Cat#553793; RRID: AB_395057
Recombinant Anti-MRP8 antibody [EPR3554]	abcam	Cat#ab92331; RRID: AB_2050283
Rabbit anti-CD56 (clone RCD56, Isotype IgG)	Zytomed Systems	Cat#RBK050; RRID: AB_2864528
APC anti-human CD105 Antibody	Biolegend	Cat#323208; RRID: AB_755960
PE anti-human CD271 (NGFR) Antibody	Biolegend	Cat#345106; RRID: AB_2152647
APC/Cyanine7 anti-human CD31 Antibody	Biolegend	Cat#303120; RRID: AB_10640734
FITC anti-human CD45 Antibody	Biolegend	Cat#368508; RRID: AB_2566368
FITC anti-human CD235ab Antibody	Biolegend	Cat#306610; RRID: AB_756046
FITC anti-human CD71 Antibody	Biolegend	Cat#334104; RRID: AB_2201482
FITC anti-human CD41 Antibody	Biolegend	Cat#303704; RRID: AB_314374
FITC anti-human CD61 Antibody	Biolegend	Cat#336404; RRID: AB_1227580
7-AAD Viability Staining Solution	Biolegend	Cat#420404
goat anti-IL-33 Antibody	R&D Systems	Cat#AF3626; RRID: AB_884269
Rabbit anti goat Antibody	DAKO	Cat#E0466
rabbit-anti-S100-Antibody	DAKO	Cat#Z0311
goat anti-rabbit-Antibody	Vector	Cat#BP-9100
Anti-Actin, α-Smooth Muscle - FITC Antibody	Sigma Aldrich	Cat#F3777; RRID: AB_476977
Bacterial and Virus Strains
pRRL.PPT.SFFV.IRES2.EGFP.WPRE	Axels Schambach, Dirk Heckl	N/A
MSCV-IRES-EGFP	Tannishtha Reya	Addgene Plasmid #20672; RRID:Addgene_20672
pMIG-JAK2WT-IRES-EGFP	Melanie Curie	N/A
pMIG-JAK2V617F-IRES-EGFP	Melanie Curie	N/A
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Murine thrombopoietin	Peprotech	Cat#351-14
Murine stem cell factor	Peprotech	Cat#250-03
Retronectin	Takara Bio	Cat#T100A/B
Polybrene	Merck Millipore	Cat#TR-1003-G
Fugene	Promega	Cat#E2691
StemSpan SFEM	Stem Cell Technologies	Cat#09600
Collagenase II	Invitrogen	Cat#17101015
Murine bFGF	Peprotech	Cat#450-33
Murine EGF	Peprotech	Cat#315-09
Recombinant murine IL-33	Peprotech	Cat#210-33
Recombinant human TGF-β1	InvivoGen	Cat#rcyc-htgfb1
Poly(ethylene glycol) BioUltra 300	Sigma	Cat#90878-250ML-F
Tasquinimod (ABR-215050)	Biorbyt	Cat#ORB251345
B-27 Supplement (50X), serum free	ThermoFisher	Cat#17504044
Forskolin	Sigma-Aldrich	Cat#F6886
Recombinant Human PDGF-AA	Peprotech	Cat#100-13A
Heregulin-β3, Epidermal growth factor (EGF) domain	Sigma-Aldrich	Cat#01-201
Liberase	Roche	Cat#5401020001
DNaseI	Sigma	Cat#DN25
Antigen unmasking solution	Vector	Cat#H-3300
Hematoxylin Solution, Gill No. 1	Sigma	Cat#GHS1128
Critical Commercial Assays
Chromium Single Cell 3′ Reagent Kits (v2)	10x Genomics	Cat#PN-120237
Chromium Single Cell A Chip Kit (v2)	10x Genomics	Cat#PN-120236
i7 Multiplex Kit, 96 rxns	10x Genomics	Cat#PN-120262
Single Cell 3′Reagent Kits (v2) User Guide	10x Genomics	Cat#CG00052, Rev D
High-Capacity cDNA Reverse Transcription Kits	Thermo Fisher	Cat#4368814
Fast SYBR Green Master Mix	Applied Biosystems	Cat#4385616
MesenCult Expansion Kit (Mouse)	STEMCELL	Cat#05513
Reticulin silver plating kit acc. to Gordon & Sweets	Sigma	Cat#1002510001
Human S100A8 DuoSet ELISA	R&D Systems	Cat#DY4570-05
Chromium Single Cell 3′ Reagent Kits (v2)	10x Genomics	Cat#PN-120237
Chromium Single Cell A Chip Kit (v2)	10x Genomics	Cat#PN-120236
i7 Multiplex Kit, 96 rxns	10x Genomics	Cat#PN-120262
Single Cell 3′Reagent Kits (v2) User Guide	10x Genomics	Cat#CG00052, Rev D
AVIDIN/BIOTIN blocking Kit	Vector	Cat#SP-2001
Peroxidase substrate Kit	Vector	Cat#SK-4100
ABC-Kit	Vector	Cat#PK-6100
Deposited Data
Genome Reference Consortium Mouse Build 38 patch release 6, mm10	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26
Raw Data	This paper	GEO: GSE156644
Analyzed Data	This paper	10.5281/zenodo.3979087
Experimental Models: Cell Lines
Hek293T	ATCC	CRL-3216; RRID:CVCL_0063
Experimental Models: Organisms/Strains
B6.SJL-Ptprca Pepcb/BoyJ Mus musculus	The Jackson Laboratory	Cat#JAX:002014; RRID:IMSR_JAX:002014
C57BL/6J Mus musculus	The Jackson Laboratory	Cat# JAX:000664; RRID:IMSR_JAX:000664
Gli1tm3(re/ERT2)Alj/J	The Jackson Laboratory	Cat#007913
Rosa26tdTomato (i.e., B6-Cg-Gt(ROSA)26Sorttm(CAG-tdTomato)Hze/J)	The Jackson Laboratory	Cat#007909
Oligonucleotides
See Table S6	See Table S6	See Table S6
Recombinant DNA
psPAX2 (lentivral packaging)	Didier Trono	Addgene Plasmid #12259; RRID:Addgene_12259
pCMV-VSV-G (lentiviral envelope)	Didier Trono	Addgene Plasmid #8454; RRID:Addgene_8454
pCL-Eco (retroviral packaging)	Novus Biologicals	Cat# NBP2-29540
Software and Algorithms
GraphPadPrism v8	GraphPad Software Inc.	RRID:SCR_002798
FlowJo v10	Tree Star Inc.	RRID:SCR_008520
Adobe Phostoshop CC 2018	Adobe Systems Inc.	RRID:SCR_014199
Adobe Illustrator CC 2018	Adobe Systems Inc.	RRID:SCR_010279
Cellranger v 2.1.1	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/2-1
Seurat (v2.3.4; v3.1.0)	Butler et al., 2018	https://satijalab.org/seurat
clusterProfiler v3.12.0	(Yu et al., 2012)	https://git.bioconductor.org/packages/clusterProfiler
edgeR v3.26.7	McCarthy et al., 2012	https://git.bioconductor.org/packages/edgeR
Monocle v2.12.0	Trapnell et al., 2014	https://git.bioconductor.org/packages/monocle
	Qiu et al., 2017
R v3.6.1	CRAN	https://www.R-project.org
Progeny v1.11.0	Schubert et al., 2018	https://github.com/saezlab/progeny
Viper v1.20.0	(Alvarez et al., 2016)	https://git.bioconductor.org/packages/viper
CellPhoneDB v2.0.5	Efremova et. al, 2020	https://github.com/Teichlab/cellphonedb
biomaRt v1.2.0	(Durinck et al., 2009)	https://git.bioconductor.org/packages/biomaRt