| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD11c (3.9), Purified | BioLegend | Cat# 301602; RRID: AB_314172 |
| CD33 (WM53), Purified | BioLegend | Cat# 303402; RRID: AB_314346 |
| CD209 (9E9A8), Purified | BioLegend | Cat# 330102; RRID: AB_1134253 |
| CD14 (M5E2), Purified | BioLegend | Cat# 301802; RRID: AB_314184 |
| CD123 (6H6), Purified | BioLegend | Cat# 306002; RRID: AB_314576 |
| CD21 (Bu32), Purified | BioLegend | Cat# 354902; RRID: AB_11219188 |
| CD192 (K036C2), Purified | BioLegend | Cat# 357202; RRID: AB_2561851 |
| CD163 (GHI/61), Purified | BioLegend | Cat# 333602; RRID: AB_1088991 |
| CD36 (5-271), Purified | BioLegend | Cat# 336202; RRID: AB_1279228 |
| CD86 (IT2.2), Purified | BioLegend | Cat# 305402; RRID: AB_314522 |
| CD169 (7-239), Purified | BioLegend | Cat# 346002; RRID: AB_2189031 |
| CD274 (29E.2A3), Purified | BioLegend | Cat# 329719; RRID: AB_2565429 |
| CD254 (MIH24), Purified | BioLegend | Cat# 347501; RRID: AB_2044062 |
| CD106 (EPR5047), Purified | Abcam | Cat# ab134047; RRID: AB_2721053 |
| CD3 (UCHT1), Purified | BioLegend | Cat# 300402; RRID: AB_314056 |
| CD49a (TS2/7), Purified | BioLegend | Cat# 328302; RRID: AB_1236385 |
| gp38 (REA446), Purified | Miltenyi Biotec | Cat# 130-107-017; RRID: AB_2653261 |
| CD80 (2D10), Purified | BioLegend | Cat# 305202; RRID: AB_314498 |
| CD34 (581), Purified | BioLegend | Cat# 343502; RRID: AB_1731898 |
| CD1a (HI149), Purified | BioLegend | Cat# 300102; RRID: AB_314016 |
| CX3CR1 (2A9-1), Purified | BioLegend | Cat# 341602; RRID: AB_1595422 |
| CD32 (FUN-2), Purified | BioLegend | Cat# 303202; RRID: AB_314334 |
| CD54 (HA58), Purified | BioLegend | Cat# 353102; RRID: AB_11204426 |
| CD195 (J418F1), Purified | BioLegend | Cat# 359102; RRID: AB_2562457 |
| CD206 (15-2), Purified | BioLegend | Cat# 321102; RRID: AB_571923 |
| S100A9 (A15105J), Purified | BioLegend | Cat# 600302; RRID: AB_2721747 |
| CD45RA (HI100), Purified | BioLegend | Cat# 304102; RRID: AB_314406 |
| CD172a (15-414), Purified | BioLegend | Cat# 372102; RRID: AB_2629807 |
| CD68 (Y1/82A), Purified | BioLegend | Cat# 333802; RRID: AB_1089058 |
| CD11b (ICRF44), 209Bi | Fluidigm | Cat# 3209003; RRID: AB_2687654 |
| CD8a (RPA-T8), Purified | BioLegend | Cat# 301053; RRID: AB_2562810 |
| CD4 (RPA-T4), Purified | BioLegend | Cat# 300502; RRID: AB_314070 |
| CD25 (BC96), Purified | BioLegend | Cat# 302602; RRID: AB_314272 |
| CD38 (HIT2), Purified | BioLegend | Cat# 303502; RRID: AB_314354 |
| CXCR3 (G025H7), Purified | BioLegend | Cat# 353733; RRID: AB_2563724 |
| FoxP3 (259D/C7), Purified | BD Biosciences | Cat# 560044; RRID: AB_1645589 |
| CD7 (CD7-6B7), Purified | BioLegend | Cat# 343111; RRID: AB_2563761 |
| Gata-3 (TWAJ), Purified | Thermo Fisher Scientific | Cat# 14-9966-82; RRID: AB_1210519 |
| CCR7 (G043H7), Purified | BioLegend | Cat# 353237; RRID: AB_2563726 |
| CCR6 (G034E3), Purified | BioLegend | Cat# 353427; RRID: AB_2563725 |
| CD27 (O323), Purified | BioLegend | Cat# 302802; RRID: AB_314294 |
| CD10 (HI10a), Purified | BioLegend | Cat# 312223; RRID: AB_2562828 |
| CD117 (104D2), Purified | BioLegend | Cat# 105814; RRID: AB_313223 |
| CCR4 (L291H4), Purified | BioLegend | Cat# 359402; RRID: AB_2562364 |
| CD161 (HP-3G10), Purified | BioLegend | Cat# 339919; RRID: AB_2562836 |
| CD185 (J252D4), Purified | BioLegend | Cat# 356902; RRID: AB_2561811 |
| RORgt (AFKJS-9), Purified | Thermo Fisher Scientific | Cat# 14-6988-82; RRID: AB_1834475 |
| CD294 (BM16), Purified | BioLegend | Cat# 350102, RRID: AB_10639863 |
| LAG-3 (7H2C65), Purified | BioLegend | Cat# 369202; RRID: AB_2616877 |
| CTLA-4 (L3D10), Purified | BioLegend | Cat# 349902; RRID: AB_10642827 |
| PD-1 (EH12.2H7), Purified | BioLegend | Cat# 329941; RRID: AB_2563734 |
| Tim-3 (F38-2E2), Purified | BioLegend | Cat# 345019; RRID: AB_2563790 |
| CD127 (A019D5), Purified | BioLegend | Cat# 351337; RRID: AB_2563715 |
| Bcl-6 (k112-91), Purified | BD Biosciences | Cat# 561520; RRID: AB_10713172 |
| T-bet (4B10), Purified | BioLegend | Cat# 644825; RRID: AB_2563788 |
| CD45RO (UCHL1), Purified | BioLegend | Cat# 304239; RRID: AB_2563752 |
| CD56 (HCD56), Purified | BioLegend | Cat# 318302; RRID: AB_604092 |
| Ki-67 (Ki-67), Purified | BioLegend | Cat# 350523; RRID: AB_2562838 |
| CD44 (BJ18), Purified | BioLegend | Cat# 338802; RRID: AB_1501199 |
| CD45 (HI30), 89Y | Fluidigm | Cat# 3089003; RRID: AB_2661851 |
| CD326 (9C4), Purified | BioLegend | Cat# 324229; RRID: AB_2563742 |
| CD19 (HIB19), Purified | BioLegend | Cat# 302202; RRID: AB_314232 |
| HLA-DR (10.1), Purified | BioLegend | Cat# 307602; RRID: AB_314680 |
| CD31 (WM59), Purified | BioLegend | Cat# 303127; RRID: AB_2563740 |
| CD16 (B73.1), Purified | BioLegend | Cat# 360702; RRID: AB_2562693 |
| CD64 (L243), Purified | BioLegend | Cat# 305029; RRID: AB_2563759 |
| Chemicals, peptides, and recombinant proteins | ||
| EQ Four Element Calibration Beads | Fluidigm | Cat# 201078 |
| Antibody Stabilizer PBS | Candor Bioscience | Cat# 131050 |
| Bond-Breaker TCEP Solution | Thermo Fisher Scientific | Cat# 77720 |
| Cell-ID Intercalator-Ir | Fluidigm | Cat# 201192B |
| Cell-ID Cisplatin-198Pt | Fluidigm | Cat# 201198 |
| Cell Acquisition Solution | Fluidigm | Cat# 201240 |
| Critical commercial assays | ||
| Transcription factor staining buffer set | Miltenyi Biotec | Cat# 130-122-981 |
| Maxpar® X8 Multimetal Antibody Labeling Kit | Fluidigm | Cat# 201300 |
| Preamp Master Mix | Fluidigm | Cat# 100-5580 |
| Reverse Transcription Master Mix | Fluidigm | Cat# 100-6298 |
| TaqMan Universal PCR Master Mix (2X) | Life Technologies | Cat# PN 4304437 |
| 96.96 DNA Binding Dye Sample/Loading Kit—10 IFCs | Fluidigm | Cat# BMK-M10-96.96-EG |
| Deposited data | ||
| CyTOF data | Chevrier et al.15 | https://doi.org/10.1016/j.xcrm.2020.100166 |
| scRNaseq sata | Wilk et al.25 | https://doi.org/10.1038/s41591-020-0944-y |
| CyTOF data | Schulte-Schrepping et al.21 | https://doi.org/10.1016/j.cell.2020.08.001 |
| CyTOF data | This paper | https://doi.org/10.17632/xg9k72r5rt.1 |
| CyTOF data | This paper | https://doi.org/10.17632/c29frc3y6s.1 |
| Clinical data | This paper | https://doi.org/10.17632/5n8df8jvk4.1 |
| Oligonucleotides | ||
| IFIT1: interferon induced protein with tetratricopeptide repeats 1 | TaqMan® Assays, ThermoFisher Scientific | Hs03027069_s1 |
| IFNAR1: interferon alpha and beta receptor subunit 1 | TaqMan® Assays, ThermoFisher ScientificThermoFisher Scientific | Hs01066116_m1 |
| ISG15: ISG15 ubiquitin-like modifier | TaqMan® Assays, ThermoFisher ScientificThermoFisher Scientific | Hs01921425_s1 |
| IFI27: interferon alpha inducible protein 27 | TaqMan® Assays, ThermoFisher Scientific | Hs01086373_g1 |
| IFI44L: interferon induced protein 44 like | TaqMan® Assays, ThermoFisher Scientific | Hs00915287_m1 |
| RSAD2: radical S-adenosyl methionine domain containing 2 | TaqMan® Assays, ThermoFisher Scientific | Hs00369813_m1 |
| IFNAR2: interferon alpha and beta receptor subunit 2 | TaqMan® Assays, ThermoFisher Scientific | Hs01022059_m1 |
| ELF1: E74-like factor 1 (ets domain transcription factor) | TaqMan® Assays, ThermoFisher Scientific | Hs00152844_m1 |
| Software and algorithms | ||
| CellCnn, ScaiVision platform | Scailyte AG | version 0.3.6 |
| R | https://cran.r-project.org | v3.6.3 |
| Premessa (R package) | https://github.com/ParkerICI/premessa | premessa 0.2.6 |
| viSNE (Cytobank) | Amir et al.61 | N/A |
| FlowSOM (Cytobank) | Van Gassen et al.62 | N/A |
| Rstudio | https://www.rstudio.com/ | v1.2.5033 |
| pheatmap (R package) | https://cran.r-project.org/web/packages/pheatmap/index.html | v1.0.12 (CRAN) |
| Cytobank | Kotecha et al.63https://www.cytobank.org | N/A |
| Kaluza | Beckman Coulter | v2.1.00002 |
| Prism (software) | https://www.graphpad.com | v8 |
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