REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Mouse CD41 (MWReg30)-143Nd	Fluidigm	Cat# 3143009C
Anti-Mouse CD45R/B220 (clone RA3-6B2)-144Nd	Fluidigm	Cat# 3144011C
Anti-Mouse CD43 (clone S11)-146Nd	Fluidigm	Cat# 3146009C
Anti-Mouse CD19 (clone 6D5)-149Sm	Fluidigm	Cat# 3149002C
Anti-Mouse CD64 (clone X54-5/7.1)-151Eu	Fluidigm	Cat# 3151012C
Anti-Mouse CD3e (clone 145-2C11)-152Sm	Fluidigm	Cat# 3152004C
Anti-Mouse CD16/32 (clone 93)-153Eu	Fluidigm	Cat# 3153011C
Anti-Mouse F4/80 (clone BM8)-159Tb	Fluidigm	Cat# 3159009C
Anti-Mouse CD11c (clone N418)-162Dy	Fluidigm	Cat# 3162017C
Anti-Mouse CD31/PECAM-1 (clone 390)-165Ho	Fluidigm	Cat# 3165013C
Anti-Mouse Nkp46 (clone 29A1.4)-167Er	Fluidigm	Cat# 3167008C
Anti-Mouse CD206/MMR (clone C068C2)-169Tm	Fluidigm	Cat# 3169021C
Anti-Mouse NK1.1 (clone PK136)-170Er	Fluidigm	Cat# 3170002C
Anti-Mouse CD11b (clone M1/70 )-172Yb	Fluidigm	Cat# 3172012C
Anti-Mouse CD117/c-kit (clone 2B8)-173Yb	Fluidigm	Cat# 3173004C
Anti-Mouse I-A/I-E (clone M5/144)-174Yb	Fluidigm	Cat# 3174003C
Anti-Mouse FceR1a (clone MAR-1)-176Yb	Fluidigm	Cat# 3176006C
FITC anti-Mouse/human CD45R/B220 (clone RA3-6B2)	BioLegend	Cat# 103205; RRID: AB_312990
AF647 anti-Mouse CD192 (CCR2) (clone SA203G11)	BioLegend	Cat# 150603; RRID: AB_2566139
PE-Cy7 anti-Mouse CD193 (CCR3) (clone J073E5)	BioLegend	Cat# 144513; RRID: AB_2565739
PE anti-Mouse CD195 (CCR5) (clone HM-CCR5)	BioLegend	Cat# 107005; RRID: AB_313300
BV421 anti-Mouse CD197 (CCR7) (clone 4B12)	BioLegend	Cat# 120119; RRID: AB_10897811
APC/Cy7 anti-Mouse/human CD11b (Mac1) (clone M1/70)	BioLegend	Cat# 101226; RRID: AB_830642
APC anti-Mouse CD206 (mannose receptor) (clone C068C2)	BioLegend	Cat# 141707; RRID: AB_10896057
PE anti-mouse CD3 (clone 17A2)	BioLegend	Cat# 100205; RRID: AB_312662
Alexa Fluor 647 anti-Mouse CD31 (clone MEC13.3)	BioLegend	Cat# 102516; RRID: AB_2161029
BV605 anti-Mouse CD31 (clone 390)	BioLegend	Cat# 102427; RRID: AB_2563982
Anti-Mouse CD34 biotin (clone RAM34)	eBioscience	Cat# 13-0341-82
PE Rat anti-Mouse CD45 (clone 30-F11)	BD Biosciences	Cat# 553081; RRID: AB_394611
BV650 anti-Mouse CD45 (clone 30-F11)	BD Horizon	Cat# 563410; RRID: AB_2738189
APC anti-Mouse CD45.1 (clone A20)	BD Biosciences	Cat# 558701; RRID: AB_1645214
PE anti-Mouse CD45.2 (clone 104)	BD Biosciences	Cat# 560695; RRID: AB_1727493
BV421 anti-Mouse CD117 (c-Kit) (clone 2B8)	BD Biosciences	Cat# 562609; RRID: AB_11154585
BV650 anti-Mouse CX3CR1 (clone SA011E11)	BioLegend	Cat# 149033; RRID: AB_2565999
PerCP-Cy5.5 anti-Mouse CD182 (CXCR2) (clone SA045E1)	BioLegend	Cat# 149605; RRID: AB_2565564
PE Dazzle594 anti-Mouse CD184 (CXCR4) (clone L276F12)	BioLegend	Cat# 146513; RRID: AB_2563682
PE-Cy5 anti-Mouse F4/80 (clone BM8)	eBioscience	Cat# 15-4801-80
PerCP-Cy 5.5 anti-Mouse Flk-1 (clone AVAS12α1)	BD Pharmingen	Cat# 560681; RRID: AB_1727524
Anti-GFP	MBL	Cat# 598; RRID: AB_591819
BV421 anti-Mouse I-A/I-E (clone M5/114.15.2)	BioLegend	Cat# 107631; RRID: AB_10900075
PE-CF594 anti-Mouse Ly-6C (clone AL-21)	BD Horizon	Cat# 562728; RRID: AB_2737749
AF700 anti-Mouse Ly-6G (clone 1A8)	BD Biosciences	Cat# 561236; RRID: AB_10611860
PE Cy7 anti-Mouse MerTK (clone DS5MMER)	eBioscience	Cat# 25-5751-80
PE anti-Mouse CD202b (Tie2/Tek) (clone TEK4)	eBioscience	Cat# 12-5987
Purified anti-mouse MerTK (clone DS5MMER)	eBioscience	Cat# 14-5751-82
Purified anti-mouse Ly6C (MaxPar ready) (clone HK1.4)	BioLegend	Cat# 128039; RRID: AB_2563783
Purified anti-mouse Ly6G (MaxPar ready) (clone 1A8)	BioLegend	Cat# 127637; RRID: AB_2563784
Purified anti-mouse Siglec F (clone 1RNM44N)	eBioscience	Cat# 14-1702-82
Chemicals, Peptides, and Recombinant Proteins
Collagenase from Clostridium histolyticum	Sigma-Aldrich	Cat# C0130; Lot# 02M1425V
Critical Commercial Assays
RNeasy micro kit	Qiagen	Cat# 74004
Deposited Data
RNA-seq	This paper	GSE130579
Experimental Models: Cell Lines
Mouse: OP9-DL1	Schmitt and Zúñiga-Pflücker, 2002	Obtained by Prof. Nancy Speck with permission from Zuniga-Plufcker
Mouse: OP9		http://www.lgcstandards-atcc.org/Search_Results.aspx?dsNav=Ntk:PrimarySearch%7cOP9%7c3%7c,Ny:True,Ro:0,N:1000552&searchTerms=OP9&geo_country=gb&redir=1
Experimental Models: Organisms/Strains
Mouse: B6.Cg-Tg(Csf1r-EGFP)1Hume/J (also known as MacGreen)	The Jackson Laboratory	https://www.jax.org/strain/018549
Mouse: B6.129P2(Cg)-Cx3cr1tm1Litt/J (also known as CX3CR1-GFP)	The Jackson Laboratory	https://www.jax.org/strain/005582
Mouse: B6.Cg-Tg(Ly6a-EGFP)G5Dzk/J	The Jackson Laboratory	https://www.jax.org/strain/012643
Mouse: B6.SJL-PtprcaPepcb/BoyCrl (also known as Ly5.1)	Charles River	https://www.criver.com/products-services/find-model/ly51-mouse?region=3671
Oligonucleotides
See Table S5 for the list of primers
Software and Algorithms
FastQC	FastQC: a quality control application for high throughput sequence data	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR (2.3)	Dobin et al., 2013; STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21	https://github.com/alexdobin/STAR
Subread-FeatureCounts (1.5.2)	Liao et al., 2014; FeatureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30	http://subread.sourceforge.net/
HiSat (2.0.4)		https://ccb.jhu.edu/software/hisat2/index.shtml
Prism Version 5	GraphPad	http://www.graphpad.com/scientific-software/prism
BD Facs Diva version 8	BD Biosciences	http://www.bdbiosciences.com/en-us
Image J	NIH	https://imagej.nih.gov/ij/
Slidebook 6	3i	https://www.intelligent-imaging.com/slidebook
FlowJo Version 8.7 and 10.1r5	Tree Star, Inc	https://www.flowjo.com/solutions/flowjo/downloads/previous-versions
MATLAB Version 2013b		N/A
FlowSOM	Cytobank, Inc	https://premium.cytobank.org/cytobank/
Other
R coding for CyTOF analysis	This paper	https://github.com/markrobinsonuzh/samanta_cytof_analysis_code