REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD8a (RPA-T8) – purified	Biolegend	Cat# 301002
CD64 (10.1) – purified	Biolegend	Cat# 305002
CD38 (HIT2) – purified	Biolegend	Cat# 303502
CD68 (Y1/82A) – purified	Biolegend	Cat# 333802
CD36 (5-271) – purified	Biolegend	Cat# 336215
CD71 (CY1G4) – purified	Biolegend	Cat# 334102
CD20 (H1(FB1)) – purified	Becton Dickinson	Cat# 555677
CD206 (15-2) – purified	Biolegend	Cat# 321112
CD13 (WM15) – purified	Biolegend	Cat# 301702
CD204 (351615) – purified	R&D Systems	Cat# MAB2708
CD123 (6H6) – purified	Biolegend	Cat# 306002
CD11b (M1/70) – purified	Biolegend	Cat# 101202
CD40 (5c3) – purified	eBioscience	Cat# 14-0409
Slamf7 (162.1) – purified	Biolegend	Cat# 331802
CD273/PD-L2 (MIH18) – purified	Biolegend	Cat# 345502
Neuropilin/CD304 (446921) – purified	R&D Systems	Cat# MAB38701
CD82 (ASL-24) – purified	Biolegend	Cat# 342102
CD274/PD-L1 (130021) – purified	R&D Systems	Cat# MAB1561
CD274/PD-L1 (E1L3N) – purified	Cell Signaling Technologies	Cat# 13684S
CD119 (GIR-208) – purified	Biolegend	Cat# 308604
CXCR4 (12G5) – purified	Biolegend	Cat# 306502
CD279/PD-1 (EH12.2H7) – purified	Biolegend	Cat# 329902
CD7 (M-T701) – purified	Becton Dickinson	Cat# 555359
CD4 (RPA-T4) – purified	Biolegend	Cat# 300516
CD32 (FUN-2) – purified	Biolegend	Cat# 303202
CD16 (3G8) – purified	Biolegend	Cat# 302002
CD14 (RMO52) – purified	Beckman Coulter	Cat# IM2580U
CD163 (GHI/61) – purified	Biolegend	Cat# 333602
CD169 (7-239) – purified	Biolegend	Cat# 346002
CD86 (233(FUN-1)) – purified	Becton Dickinson	Cat# 555655
HLA-ABC (W6/32) – purified	Biolegend	Cat# 311402
CD81 (5A6) – purified	Biolegend	Cat# 349502
CD88 (S5/1) – purified	Biolegend	Cat# 344302
HLA-DR (L243) – purified	Biolegend	Cat# 307602
CD54 (HA58) – purified	Biolegend	Cat# 353102
CD15 (HI98) – purified	Biolegend	Cat# 301902
CD80 (2D10) – purified	Biolegend	Cat# 305202
CD28 (CD28.2) – purified	eBioscience	Cat# 16-0289
Tim-3 (F38-2E2) – purified	Biolegend	Cat# 345035
LAG-3 (333210) – purified	R&D Systems	Cat# MAB23193
CTLA-4 (L3D10) – purified	Biolegend	Cat# 349902
CD278/ICOS (C398.4A) – purified	Biolegend	Cat# 313502
CD134/OX40 (Ber-ACT35) – purified	Biolegend	Cat# 350002
4-1BB ((4B4-1) – purified	Biolegend	Cat# 309802
GITR (621) – purified	Biolegend	Cat# 311602
CD3 (UCHT1) – purified	Biolegend	Cat# 300402
CD25 (M-A251) – purified	Biolegend	Cat# 356102
Ki-67 (8D5) – purified	Cell Signaling Technologies	Cat# 9449
CD45 (HI30) – purified	Biolegend	Cat# 304002
CD45RA (HI100) – purified	Biolegend	Cat# 304102
CD11c (Bu15) – purified	Biolegend	Cat# 337221
CD127 (A019D5) – purified	Biolegend	Cat# 351302
Foxp3 (PCH101) - Dy162	Fluidigm	Cat# 3162011A
CD197/CCR7 (G043H7) - Sm159	Fluidigm	Cat# 3159003A
CD38 (EPR4106) – purified	Abcam	Cat# ab176886
Foxp3 (236A/E7) – purified	eBioscience	Cat# 14-4777-82
PD-1 (D4W2J) – purified	Cell Signaling	Cat# 86163S
CD8 (4B11) – purified	Bio-Rad	Cat# MCA1817T
Anti-mouse IgG1, 2a, 3 (Fc fragment) - HRP	Jackson Immuno	Cat# 115-035-164
anti-goat IgG (H+L) - HRP	SantaCruz	Cat# sc-2020
anti-rabbit IgG (minimal x-reactivity) - HRP	Biolegend	Cat# 406401
Biological Samples
Buffy Coat	Zurich Blood Transfusion Service	N/A
Clear cell renal cell carcinoma samples	University Health Network (UHN) Biospecimen Sciences Program and the Cooperative Health Tissue Network (CHTN)	N/A
Chemicals, Peptides, and Recombinant Proteins
M-CSF	PeproTech	Cat# 300-25
LPS	Sigmal Aldrich	Cat# L2654
IL10	Peprotech	Cat# 200-10
Ovalbumin	Sigma Aldrich	Cat# C6534
α-chicken	Sigma Aldrich	Cat# A5503
Paraformaldehyde	Electron Microscopy Sciences	Cat# 15710
Alexa Fluor 700 NHS Ester	Molecular Probes	Cat# 20010
Alexa Fluor 750 NHS Ester	Molecular Probes	Cat# 20011
Monocyte isolation Kit	Miltenyi Biotech	Cat# 130-096-537
Bromoacetamidobenzyl-EDTA (BABE)	Dojindo Laboratories	Cat# B437-10
Maleimido mono amide DOTA (mDOTA)	Macrocyclics	Cat# B-272
Cisplatin	Fluidigm	Cat# 201064
Iridium	Fluidigm	Cat# 201192A
Maxpar X8 Multimetal labeling kit	Fluidigm	Cat# 201300
Lanthanide (III) metal isotopes as chloride salts	Fluidigm	N/A
FcR Blocking Reagent, human	Miltenyi Biotech	Cat# 130-059-901
Zombie NIR dye	Biolegend	Cat# 423105
Trilogy buffer	CellMarque	Cat# 920P-04
Critical Commercial Assays
LEGENDScreen Human Cell Screening (PE) Kit	Biolegend	cat # 700001
SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian	ThermoFischer	Cat# KIT0204
High Sensitivity NGS Fragment Analysis Kit	Advanced Analytical	Cat# DNF-474
Opal 7-Color Fluorescent IHC Kit	PerkinElmer	Cat# OP7DS1001KT
Deposited Data
RNA-sequencing data	This paper	ArrayExpress: E-MTAB-5640
Mass cytometry data	This paper	https://premium.cytobank.org/cytobank/projects/875
Software and Algorithms
FlowJo v10.0.7	N/A	https://www.flowjo.com/
Cytobank	Kotecha et al., 2010	https://www.cytobank.org/
Concatenation tool	Cytobank	https://support.cytobank.org/hc/en-us/articles/206336147-FCS-file-concatenation-tool
Normalizer	Finck et al., 2013	https://github.com/nolanlab/bead-normalization/releases
Single cell debarcoder	Zunder et al., 2015	https://github.com/nolanlab/single-cell-debarcoder
t-SNE	van der Maaten and Hinton, 2008	https://github.com/jkrijthe/Rtsne
PhenoGraph	Levine et al., 2015	https://github.com/jacoblevine/PhenoGraph
Diffusion map	Angerer et al., 2016	https://cran.r-project.org/web/packages/diffusionMap/index.html
Correspondence Analysis	Härdle and Simar, 2003	https://gist.github.com/jacoblevine/2e91ff5ccad671d4ba716c3f941ec296
Lifelines	Davidson-Pilon, 2016	https://github.com/CamDavidsonPilon/lifelines/
Survival (R package)	N/A	https://cran.r-project.org/web/packages/survival/index.html
STAR 2.5.2b	Dobin et al., 2013	https://github.com/alexdobin/STAR
fastq-screen 0.9.5	N/A	http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
QuasR 1.14.0	Gaidatzis et al., 2015	http://bioconductor.org/packages/release/bioc/html/QuasR.html
edgeR 3.16.5	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
R 3.3.2	R Development Core Team, 2015	https://www.R-project.org