REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CyTOF: anti-CD45-089Y (30-F11)	Fluidigm	Cat#3089005B RRID: N/A
CyTOF: rat anti-mouse Ly-6G-141Pr (1A8)	Fluidigm	Cat#3141008B; RRID:AB_2814678
CyTOF: anti-mouse CD11c-142Nd (N418)	Fluidigm	Cat#3142003B; RRID:AB_281473
CyTOF: anti-mouse CD45R-144Nd (RA3-6B2)	Fluidigm	Cat#3144011B; RRID:AB_2811239
CyTOF: anti-mouse CD4-145Nd (RM4-5)	Fluidigm	Cat#3145002B; RRID:AB_2687832
CyTOF: rat anti-mouse CD11b-148Nd (M1/70)	Fluidigm	Cat#3148003B; RRID:AB_2814738
CyTOF: rat anti-mouse CD44-150Nd (IM7)	Fluidigm	Cat#3150018B; RRID:AB_2827882
CyTOF: rat anti-CD25-151Eu (3C7)	Fluidigm	Cat#3151007B; RRID:AB_2827880
CyTOF: anti-mouse CD3e-152Sm (145-2C11)	Fluidigm	Cat#3152004B; RRID:AB_2687836
CyTOF: anti-mouse PD-L1-153Eu (10F.9G2)	Fluidigm	Cat#3153016B; RRID:AB_2687837
CyTOF: anti-CTLA-4-154Sm (UC10-4B9)	Fluidigm	Cat#3154008B RRID: N/A
CyTOF: anti-mouse PD-1-159Tb (29F.1A12)	Fluidigm	Cat#3159024B; RRID:AB_2687839
CyTOF: anti-Ly-6C-162Dy (HK1.4)	Fluidigm	Cat#3162014B RRID: N/A
CyTOF: anti-mouse CX3CR1-164Dy (SA011F11)	Fluidigm	Cat#3164023B; RRID:AB_2832247
CyTOF: anti-NK1.1-165Ho (PK136)	Fluidigm	Cat#3165018B RRID: N/A
CyTOF: rat anti-mouse ckit-166Er (2B8)	Fluidigm	Cat#3166004B; RRID:AB_2801435
CyTOF: rat anti-mouse CD8a-168Er (53-6.7)	Fluidigm	Cat#3168003B; RRID:AB_2811241
CyTOF: anti-CD86-172Yb (GL1)	Fluidigm	Cat#3172016B RRID: N/A
CyTOF: anti-I-A/I-E-209Bi (M5/114.15.2)	Fluidigm	Cat#3209006B RRID: N/A
CITE-seq: rat anti-CCR2/CD192 (SA203G11)	BioLegend	Cat#150625; RRID:AB_2783122
CITE-seq: rat anti-CD117/c-kit (2B8)	BioLegend	Cat#105843; RRID:AB_2749960
CITE-seq: rat anti-CD11b (M1/70)	BioLegend	Cat#101265; RRID:AB_2734152
CITE-seq: armenian hamster anti-CD11c (N418)	BioLegend	Cat#117355; RRID:AB_2750352
CITE-seq: rat anti-CD172a/SIRPα (P84)	BioLegend	Cat#144033; RRID:AB_2800670
CITE-seq: rat anti-CD25 (PC61)	BioLegend	Cat#102055; RRID:AB_2749982
CITE-seq: rat anti-CD3 (17A2)	BioLegend	Cat#100251; RRID:AB_2750533
CITE-seq: rat anti-CD38 (90)	BioLegend	Cat#102733; RRID:AB_2750556
CITE-seq: rat anti-CD4 (RM4-5)	BioLegend	Cat#100569; RRID:AB_2749956
CITE-seq: rat anti-CD44 (IM7)	BioLegend	Cat#103045; RRID:AB_2734154
CITE-seq: rat anti-CD45 (30-F11)	BioLegend	Cat#103159; RRID:AB_2734156
CITE-seq: rat anti-CD45R/B220 (RA3-6B2)	BioLegend	Cat#103263; RRID:AB_2734158
CITE-seq: rat anti-CD86 (GL-1)	BioLegend	Cat#105047; RRID:AB_2750348
CITE-seq: rat anti-CD8a (53-6.7)	BioLegend	Cat#100773; RRID:AB_2734151
CITE-seq: mouse anti-CD90.1 (OX-7)	BioLegend	Cat#202547; RRID:AB_2783141
CITE-seq: mouse anti-Cx3cr1 (SA011F11)	BioLegend	Cat#149041; RRID:AB_2783121
CITE-seq: rat anti-F4/80 (BM8)	BioLegend	Cat#123153; RRID:AB_2749986
CITE-seq: rat anti-I-A/I-E (M5/114.15.2)	BioLegend	Cat#107653; RRID:AB_2750505
CITE-seq: rat anti-Ly6C (HK1.4)	BioLegend	Cat#128047; RRID:AB_2749961
CITE-seq: rat anti-Ly6G (1A8)	BioLegend	Cat#127655; RRID:AB_2749962
CITE-seq: mouse anti-NK1.1 (PK136)	BioLegend	Cat#108755; RRID:AB_2750536
CITE-seq: rat anti-PD-1 (RMP1-30)	BioLegend	Cat#109123; RRID:AB_2734169
CITE-seq: rat anti-PD-L1 (MIH6)	BioLegend	Cat#153604; RRID:AB_2783125
CITE-seq: rat anti-CD169/Siglec-1 (3D6.112)	BioLegend	Cat#142425; RRID:AB_2783106
CITE-seq: rat anti-Siglec-H (551)	BioLegend	Cat#129615; RRID:AB_275053
CITE-seq: mouse anti-TMEM119 (A16075D)	BioLegend	Cat#853303; RRID:AB_2801201
CITE-seq: mouse anti-XCR1 (Zet)	BioLegend	Cat#148227; RRID:AB_2783120
CITE-seq: rat anti-CD24 (M1/69)	BioLegend	Cat#101841; RRID:AB_2750380
CITE-seq: rat armenian hamster anti-CD103 (2e7)	BioLegend	Cat#121437; RRID:AB_2750349
CITE-seq: rat anti-CD49d (R1-2)	BioLegend	Cat#103623; RRID:AB_2734159
CITE-seq: rat anti-mouse Hashtag 1 antibody (M1/42; 30-F11)	BioLegend	Cat#155801; RRID:AB_2750032
CITE-seq: rat anti-mouse Hashtag 2 antibody (M1/42; 30-F11)	BioLegend	Cat#155803; RRID:AB_2750033
CITE-seq: rat anti-mouse Hashtag 3 antibody (M1/42; 30-F11)	BioLegend	Cat#155805; RRID:AB_2750034
CITE-seq: rat anti-mouse Hashtag 4 antibody (M1/42; 30-F11)	BioLegend	Cat#155807; RRID:AB_2750035
CITE-seq: rat anti-mouse Hashtag 5 antibody (M1/42; 30-F11)	BioLegend	Cat#155809; RRID:AB_2750036
CITE-seq: rat anti-mouse Hashtag 6 antibody (M1/42; 30-F11)	BioLegend	Cat#155811; RRID:AB_2750037
CITE-seq: rat anti-mouse Hashtag 7 antibody (M1/42; 30-F11)	BioLegend	Cat#155813; RRID:AB_2750039
CITE-seq: rat anti-mouse Hashtag 8 antibody (M1/42; 30-F11)	BioLegend	Cat#155815; RRID:AB_2750040
Chemicals, peptides, and recombinant proteins
Bovine serum albumin	VWR Chemicals	Cat#97061-422 RRID: N/A
Cell-ID Cisplatin	Fluidigm	Cat#201064 RRID: N/A
Cell-ID Intercalator	Fluidigm	Cat#201192B RRID: N/A
Cell Staining Buffer	BioLegend	Cat#20201 RRID: N/A
Dulbecco’s PBS (D-PBS), 1×, +Ca, +Mg	Caisson Labs	Cat#PBL02-500M RRID: N/A
Ethylenediaminetetra-acetic acid disodium salt dihydrate (EDTA)	VWR Chemicals	Cat#97061-022 RRID: N/A
FcR Blocking Reagent, mouse	Miltenyi Biotec	Cat#130-092-575 RRID: N/A
Hanks Balanced Salt Solution (HBSS), 1×, -CaCl2, -MgCl2, -MgSO4, +Phenol Red	Thermo Fisher Scientific	Cat#14170161 RRID: N/A
Hanks Balanced Salt Solution (HBSS), 1×, -Ca, -Mg, -Phenol Red	Cytiva Life Sciences	Cat#SH30588.02 RRID: N/A
Hanks Balanced Salt Solution (HBSS), 10×, -CaCl2, -MgCl2, -MgSO4, -Phenol Red	Thermo Fisher Scientific	Cat#14185052 RRID: N/A
Phosphate Buffered Saline (PBS), 1×, -Ca, -Mg, -Phenol Red	Cytiva Life Sciences	Cat#SH3025602 RRID: N/A
Maxpar Cell Staining Buffer	Fluidigm	Cat#201068 RRID: N/A
MaxPar Fix and Perm Buffer	Fluidigm	Cat#201067 RRID: N/A
Maxpar PBS	Fluidigm	Cat#201058 RRID: N/A
MaxPar Water	Fluidigm	Cat#201069 RRID: N/A
Percoll	GE Healthcare	Cat#17-0891-02 RRID: N/A
RPMI 1640	Thermo Fisher Scientific	Cat#11875093 RRID: N/A
Tween 20	VWR Chemicals	Cat#97062-332 RRID: N/A
1× EQ beads	Fluidigm	Cat#201078 RRID: N/A
Critical commercial assays
Chromium Single Cell 3’ Library and Gel Bead Kit v3	10x Genomics	PN-10000092 RRID: N/A
Single Cell 3’ GEM Library and Gel Bead Kit v3.1	10x Genomics	PN-10000092 RRID: N/A
Chromium Chip B Single Cell Kit	10x Genomics	PN-1000074 RRID: N/A
Chromium i7 Multiplex Kit	10x Genomics	PN-120262 RRID: N/A
Multi-tissue Dissociation Kit I	Miltenyi Biotec	130-110-201 RRID: N/A
Deposited data
Mouse CITE-seq data	(Guldner et al., 2020)	GSE134285
Experimental models: cell lines
E0771	CH3 BioSystems	SKU:940001-Vial RRID: N/A
Experimental models: organisms/strains
C57BL/6	Jackson Laboratories	Stock#:000664 RRID: N/A
Oligonucleotides
Primer: ADT_TruSeq_i7_UDI01 - CAAGCAGAAGACGGCATACG AGAACCGCGGGTGACTGGAGTT CCTTGGCACCCGAGAATTCCA	This paper	N/A
Primer: ADT_TruSeq_i7_UDI04 - CAAGCAGAAGACGGCATACG AGTTGGACTTGTGACTGGAGT TCCTTGGCACCCGAGAATTCCA	This paper	N/A
Primer: ADT-RPI-1 - CAAGCAGAAGA CGGCATACGAGATCGTGATGTGACT GGAGTTCCTTGGCACCCGAGAATTCCA	This paper	N/A
Primer: ADT-RPI-2 - CAAGCAGAAGAC GGCATACGAGATACATCGGTGACTG GAGTTCCTTGGCACCCGAGAATTCCA	This paper	N/A
Primer: HTO_Nextera_i7_UDP01 -CAAG CAGAAGACGGCATACGAGATCGCTCA GTGTGACTGGAGTTCAGACGTGTGC	This paper	N/A
Primer: HTO_Nextera_i7_UDP02 - CAAG CAGAAGACGGCATACGAGATTATCTG ACGTGACTGGAGTTCAGACGTGTGC	This paper	N/A
Primer: HTO_Nextera_i7_UDP03 - CAAG CAGAAGACGGCATACGAGATATATGA GAGTGACTGGAGTTCAGACGTGTGC	This paper	N/A
Primer: HTO_Nextera_i7_UDP04 - CAA GCAGAAGACGGCATACGAGATCTTA TGGAGTGACTGGAGTTCAGACGTGTGC	This paper	N/A
Primer: HTO-N701 - CAAGCAGA AGACGGCATACGAGATTCGCC TTAGTGACTGGAGTTCAGACGT GTGC	This paper	N/A
Primer: HTO-N702 - CAAGCAGAA GACGGCATACGAGATCTAGTACG GTGACTGGAGTTCAGACGTGTGC	This paper	N/A
Software and algorithms
FlowJo	BD	https://www.flowjo.com
R studio	(Ihaka and Gentleman, 1996)	https://rstudio.com
CellRanger 3.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Cytobank Premium	Beckman Coulter	https://cytobank.org
GraphPad Prism	GraphPad Software	https://www.graphpad.com
Seurat_3.1.1	(Satija et al., 2015)	https://satijalab.org/seurat/
Other
CyTOF2	Fluidigm	N/A
Illumina NovaSeq 6000	Illumina	N/A
10× Chromium Controller and Accessory Kit	10x Genomics	PN-120223