Table 1.
List of reagents and resources.
| Reagent or Resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Anti-human CD1c PE/Cy7 (clone L1619) | Biolegend | Cat#: 331515; RRID: AB_1953227 |
| Anti-human CD4 APC (clone OKT4) | Biolegend | Cat#:317415; RRID: AB_571944 |
| Anti-human CD11c BUV737 (clone B-ly6) | BD Biosciences | Cat#:741827; RRID: AB_2871162 |
| Anti-human CD40Pe/Cy7 (clone HB14) | Biolegend | Cat#:311011; RRID: AB_2563922 |
| Anti-human CD45 BUV395 (clone HI30) | BD Biosciences | Cat#:563791; RRID: AB_2869519 |
| Anti-human CD45 BUV805 (clone HI30) | BD Biosciences | Cat#:612891; RRID: AB_2870179 |
| Anti-human CD45 PerCP (clone 2D1) | Biolegend | Cat#:304025; RRID: AB_893341 |
| Anti-human CD45RA BV510 (clone HI100) | Biolegend | Cat#:304141; RRID: AB_2561384 |
| Anti-human CD56 BV421 (clone HCD-56) | Biolegend | Cat#:318327; RRID: AB_10900228 |
| Anti-human CD62L BV605 (clone DREG-56) | Biolegend | Cat#:304833; RRID: AB_2562129 |
| Anti-human CD69 BUV737 (clone FN50) | BD Biosciences | Cat#:612818 |
| Anti-human CD80 BUV395 (clone L307) | BD Biosciences | Cat#:565210; RRID: AB_2739112 |
| Anti-human CD83 BV711 (clone HB15e) | BD Biosciences | Cat#:740802; RRID: AB_2740465 |
| Anti-human CD86 BV421 (clone IT2.2) | Biolegend | Cat#:305425; RRID: AB_10899582 |
| Anti-human CD86 BV605 (clone 2331) | BD Biosciences | Cat#:562999; RRID: AB_2737941 |
| Anti-human CD123 BV650 (clone 6H6) | Biolegend | Cat#:306019; RRID: AB_11218792 |
| Anti-human CD141 BV711 (clone 1A4) | BD Biosciences | Cat#:563155; RRID: AB_2738033 |
| Anti-human CD197 (CCR7) PE (clone G043H7) | Biolegend | Cat#:353203; RRID: AB_10916391 |
| Anti-human CD197 (CCR7) PerCPeFluor710 (clone 3D12) | ThermoFisher | Cat#:46-1979-42; RRID: AB_10853814 |
| Anti-human CD252 (OX-40L) BV421 (clone ik-1) | BD Biosciences | Cat#:563766; RRID: AB_2738412 |
| Anti-human CD253 (TRAIL) APC (clone RIK-2) | Biolegend | Cat#:308209; RRID: AB_2564397 |
| Anti-human CD274 (PD-L1) BV605 (clone MIH1) | BD Biosciences | Cat#:563469 |
| Anti-human CD303 (CLEC4C) APC (clone 201A) | Biolegend | Cat#:354205; RRID: AB_11147168 |
| Anti-human CD304 BV510 (clone 12C2) | Biolegend | Cat#:354515; RRID: AB_2563074 |
| Anti-human CD304 PerCP Cy5.5 (clone 12C2) | Biolegend | Cat#:354509; RRID: AB_2561558 |
| Anti-human CD314 (NKG2D) BV711 (clone P30-15) | Biolegend | Cat#:320802; RRID: AB_492956 |
| Anti-human CD327 (SIGLEC6) APC (clone 767329) | R&D Systems | Cat#:FAB2859A |
| Anti-human CD370 (CLEC9A) APC (clone M80) | Biolegend | Cat#:35805; RRID: AB_2565518 |
| Anti-human AXL PE (clone 108724) | R&D Systems | Cat#:FAB154P |
| Anti-human HLA-ABC BUV661 (clone G46-2.6) | BD Biosciences | Cat#:741621; RRID: AB_2871027 |
| Anti-human HLA-DR BV711 (clone L243) | BD Biosciences | Cat#:563696; RRID: AB_2738378 |
| Anti-human IFN-α2 FITC (clone MMHA-1) | PBL Assay Science | Cat#:21112-3 |
| Anti-human lineage (CD3, CD14, CD16, CD19, CD20, CD56) FITC (clones OKT3; M5E2; 3G8; HIB19; 2H7; HCD56) | Biolegend | Cat#:348801; RRID: AB_10612570 |
| Human Fc Receptor Blocking Solution (TrueStain FcX) | Biolegend | Cat#422302 |
| Biological samples | ||
| Human peripheral blood mononuclear cells (PBMCs) | Roche Diagnostics Medical Service | N/A |
| Human cord blood CD34+ hematopoietic stem and progenitor cells (HSCs) | Lonza | Cat#:2C-101 |
| Tumor digests from patients | Discovery Life Science | N/A |
| Tumor pieces from patients | Fidelis | N/A |
| Tumor pieces from patients | Indivumed | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| 2-Mercaptoethanol | PAN Biotech | Cat#:P07-05020 |
| Accutase | PAN Biotech | Cat#:P10-2110M |
| Albumin from bovine serum 30% | Sigma-Aldrich | Cat#:A9576 |
| Collagenase IV | Worthington | Cat#:LS0004186 |
| CpG-A ODN 2216 TLR9 | Invivogen | Cat#:tlrl-2216 |
| DNAse I, type 4 | Sigma-Aldrich | Cat#:D5025 |
| DPBS (1x) | PAN Biotech | Cat#:P04-36500 |
| DMSO | Sigma-Aldrich | Cat#:D8418 |
| heat-inactivated FBS | Anprotech | |
| hepes buffer | Sigma-Aldrich | Cat#:51558 |
| human serum albumin | Sigma-Aldrich | Cat#:SRP6182 |
| Hyaluronidase | Sigma-Aldrich | Cat#:H3506 |
| L-ascorbic acid | Sigma-Aldrich | Cat#:A92902 |
| L-glutamin | Anprotech | AC-AS-0001 |
| MEM-α with nucleosides | GIBCO | Cat#:12571063 |
| MEM non-essential amino acid | PAN Biotech | Cat#:P08-32100 |
| MEM vitamin solution | PAN Biotech | Cat#:11120052 |
| Mitomycin C | Sigma-Aldrich | Cat#:M4287 |
| penicillin/streptomycin | Anprotech | Cat#:P06-07100 |
| R848 Resiquimod | Invivogen | Cat#:tlrl-r848 |
| Recombinant human FLT3-ligand | Peprotech | Cat#:300-19 |
| Recombinant human GM-CSF (carrier-free) | Biolegend | Cat#:572905 |
| Recombinant human IFN-β | Peprotech | Cat#:AF-300-02B |
| Recombinant human IFN-γ | Peprotech | Cat#:300-02BC |
| Recombinant human IL-3 | Peprotech | Cat#:200-03 |
| Recombinant human IL-7 | Peprotech | 200-07 |
| Recombinant human SCF | Peprotech | Cat#:AF-300-07 |
| Recombinant human TPO | Peprotech | Cat#:300-18 |
| RPMI 1640 | PAN Biotech | Cat#:P04-16500 |
| SFEM II stem pan medium | Stemcell Technologies | Cat#:09605 |
| sodium pyruvate | Anprotech | Cat#:P04-43100 |
| Stem Regenin 1 | Biogems | Cat#:1224999 |
| TLR7 agonist RO7117419 | Roche Diagnostics | N/A |
| Viastain AO staining solution | Nexcelom Biosciences | Cat#:CS2-0106 |
| Zombie UV fixable viability kit | Biolegend | Cat#:423107 |
| Critical commercial assays | ||
| Chromium next GEM automated single cell 5’ Kit v2, module 1 | 10x Genomics | Cat#:1000292 |
| Chromium next GEM automated single cell 5’ Kit v2, module 2 | 10x Genomics | Cat#:1000295 |
| Chromium next GEM automated single cell 5’ Kit v2, module 3 | 10x Genomics | Cat#:1000294 |
| Cytokine & chemokine 34-plex human ProcartaPlex panel | Thermo Fisher | Cat#:EPX340-12167-901 |
| EasySep human NK cell enrichment kit | Stemcell Technologies | Cat#:19055 |
| Foxp3 staining buffer set | BD Biosciences | Cat#:562725 |
| IL-29 IFN lambda 1 human ProcartaPlex simplex kit | Thermo Fisher | Cat#:EPX01A-12049-901 |
| Human CD8/NK Legendplex assay | Biolegend | Cat#:741187 |
| Next GEM chip K & gaskets automated single cell | 10x Genomics | Cat#:PN-1000297 |
| Pan-IFN-α ELISA | PBL Assay Science | Cat#:41115-1 |
| Pan-DC enrichment kit | Miltenyi Biotec | Cat#:130-100-777 |
| Plasmacytoid dendritic cell isolation kit II, human | Miltenyi Biotec | Cat#:130-097-415 |
| ProcartaPlex human basic kit | ThermoFisher | Cat#:EPX010-10420-901 |
| Experimental models: Cell lines | ||
| MS-5 | DSMZ | RRID: CVCL_2128 |
| Software and algorithms | ||
| Bio-Plex manager v6.2.0.175 | Bio-Rad | https://www.bio-rad.com/de-de/category/bio-plex-software |
| Besca package v2.4 | Roche Diagnostics | https://bedapub.github.io/besca/ |
| Bioconductor v3.15 | Bioconductor | https://bioconductor.org/ |
| Cell ranger single cell v6.0.2 | 10x Genomics | https://www.10xgenomics.com/support/software/cell-ranger/downloads |
| EdgeR v3.38.0, v3.40.2 | Bioconductor package | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| Fgsea v1.24.0 | Bioconductor package | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| FlowJo v10.8.1. | BD Biosciences | https://www.flowjo.com/solutions/flowjo/downloads |
| ggplot2 v3.3.6 | R package | https://github.com/tidyverse/ggplot2 |
| Graph Pad Prism v8 | GraphPad Software | https://www.graphpad.com/ |
| GSVA v1.46.0 | Bioconductor package | https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| pheatmap v1.0.12 | R package | https://CRAN.R-project.org/package=pheatmap |
| UpSetR v1.4.0 | R package | https://CRAN.R-project.org/package=UpSetR |
| R v4.2.0 | Microsoft Corporation | https://www.R-project.org/ |