Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Homo sapiens) | Primary peripheral blood mononuclear cells | BioIVT, Westbury, NY, USA | SERATRIALS-18002; sample BRH1291132 | WIRB protocol # 20190318; Ficoll-purified |
| Biological sample (Homo sapiens) | Primary peripheral blood mononuclear cells | BioIVT, Westbury, NY, USA | SERATRIALS-18002; sample HMN85396 | WIRB protocol # 20190318; leukapheresis-purified |
| Biological sample (Homo sapiens) | Primary peripheral blood mononuclear cells | BioIVT, Westbury, NY, USA | SERATRIALS-18002; sample RG1131 | WIRB protocol # 20190318; Ficoll-purified |
| Biological sample (Homo sapiens) | Primary peripheral nlood mononuclear cells | Bloodworks NW, Seattle, WA, USA | BT001; sample 5716BW | WIRB protocol # 20141589; Ficoll-purified |
| Biological sample (Homo sapiens) | Primary peripheral blood mononuclear cells | Bloodworks NW, Seattle, WA, USA | BT001; sample 7811BW | WIRB protocol # 20141589; Ficoll-purified |
| Antibody | Biotin anti-human CD15 (SSEA-1) antibody (mouse monoclonal) | BioLegend | Cat# 301913, RRID:AB_2561325 | (0.15 µL per million cells) |
| Antibody | BUV395 anti-human CD14 antibody (mouse monoclonal) | BD Biosciences | Cat# 563561, RRID:AB_2744288 | (1 µL per million cells) |
| Antibody | BUV496 mouse anti-human CD45 antibody (mouse monoclonal) | BD Biosciences | Cat# 750179, RRID:AB_2868405 | (1 µL per million cells) |
| Antibody | BUV563 mouse anti-human CD15 antibody (mouse monoclonal) | BD Biosciences | Cat# 741417, RRID:AB_2868406 | (1 µL per million cells) |
| Antibody | BUV615 mouse anti-human CD56 antibody (mouse monoclonal) | BD Biosciences | Cat# 613001, RRID:AB_2868413 | (2 µL per million cells) |
| Antibody | Brilliant Violet 650 anti-human CD3 antibody (mouse monoclonal) | BioLegend | Cat# 300468, RRID:AB_2629574 | (2 µL per million cells) |
| Antibody | Mouse anti-human CD19 High Parameter Custom Antibody BB790-P Conjugate (mouse monoclonal) | BD Biosciences | Cat# 624296 | Custom reagent; conjugate of mouse anti-human CD19 (clone HIB19) and BB790-P (1 µL per million cells) |
| Antibody | PE/Cy5 anti-human CD16 antibody (mouse monoclonal) | BioLegend | Cat# 302009, RRID:AB_314209 | (1 µL per million cells) |
| Antibody | BUV395 mouse anti-human CD3 antibody (mouse monoclonal) | BD Biosciences | Cat# 563546, RRID:AB_2744387 | Custom reagent; conjugate of mouse anti-human CD3 (clone UCHT1) and BUV395 (1:50 in 100 µL volume) |
| Antibody | Mouse anti-human CD45RA High Parameter Custom Antibody BUV615-P Conjugate (mouse monoclonal) | BD Biosciences | Cat# 624297 | Custom reagent; conjugate of mouse anti-human CD45RA (clone HI100) and BUV615-P (1:5 in 100 µL volume) |
| Antibody | BUV661 mouse anti-human CD14 antibody (mouse monoclonal) | BD Biosciences | Cat# 741684, RRID:AB_2868407 | (1:50 in 100 µL volume) |
| Antibody | BUV737 mouse anti-human CD8 antibody (mouse monoclonal) | BD Biosciences | Cat# 749367, RRID:AB_2868408 | (1:5 in 100 µL volume) |
| Antibody | BUV805 mouse anti-human CD11c antibody (mouse monoclonal) | BD Biosciences | Cat# 742005, RRID:AB_2868409 | (1:33 in 100 µL volume) |
| Antibody | BV421 mouse anti-human CD25 antibody (mouse monoclonal) | BD Biosciences | Cat# 562442, RRID:AB_11154578 | (1:50 in 100 µL volume) |
| Antibody | BV480 mouse anti-human CD4 (mouse monoclonal) | BD Biosciences | Cat# 566104, RRID:AB_2739506 | (1:5 in 100 µL volume) |
| Antibody | BV605 mouse anti-Human CD16 (FcγRIII) antibody (mouse monoclonal) | BD Biosciences | Cat# 563172, RRID:AB_2744297 | (1:50 in 100 µL volume) |
| Antibody | Brilliant Violet 650 anti-human CD123 antibody (mouse monoclonal) | BioLegend | Cat# 306020, RRID:AB_2563827 | (1:50 in 100 µL volume) |
| Antibody | Brilliant Violet 711 anti-human CD127 (IL-7Rα) antibody (mouse monoclonal) | BioLegend | Cat# 351328, RRID:AB_2562908 | (1:50 in 100 µL volume) |
| Antibody | BV750 mouse anti-human IgD antibody (mouse monoclonal) | BD Biosciences | Cat# 747484, RRID:AB_2868411 | (1:20 in 100 µL volume) |
| Antibody | BV786 mouse anti-human neuropilin-1 (CD304) antibody (mouse monoclonal) | BD Biosciences | Cat# 743132, RRID:AB_2741299 | (1:50 in 100 µL volume) |
| Antibody | BB515 mouse anti-human CD141 antibody (mouse monoclonal) | BD Biosciences | Cat# 565084, RRID:AB_2739058 | (1:33 in 100 µL volume) |
| Antibody | CD11b monoclonal antibody, PerCP-Cy5.5 conjugated (rat monoclonal) | BD Biosciences | Cat# 561114, RRID:AB_2033995 | (1:5 in 100 µL volume) |
| Antibody | PE anti-human CD27 antibody (mouse monoclonal) | BioLegend | Cat# 302808, RRID:AB_314300 | (1:20 in 100 µL volume) |
| Antibody | PE/Dazzle 594 anti-human TCRα/βantibody (mouse monoclonal) | BioLegend | Cat# 306726, RRID:AB_2566599 | (1:33 in 100 µL volume) |
| Antibody | Mouse anti-CD34 monoclonal antibody, PE-Cy5 conjugated (mouse monoclonal) | BD Biosciences | Cat# 555823, RRID:AB_396152 | (1:20 in 100 µL volume) |
| Antibody | PE/Cy7 anti-human CD197 (CCR7) antibody (mouse monoclonal) | BioLegend | Cat# 353226, RRID:AB_11126145 | (1:33 in 100 µL volume) |
| Antibody | APC anti-human CD38 antibody (mouse monoclonal) | BioLegend | Cat# 356606, RRID:AB_2561902 | (1:20 in 100 µL volume) |
| Antibody | APC-R700 mouse anti-human CD56 (NCAM-1) antibody (mouse monoclonal) | BD Biosciences | Cat# 565139, RRID:AB_2744429 | (1:20 in 100 µL volume) |
| Antibody | APC/Cyanine7 anti-human HLA-DR antibody (mouse monoclonal) | BioLegend | Cat# 307618, RRID:AB_493586 | (1:20 in 100 µL volume) |
| Antibody | TotalSeq-A0062 anti-human CD10 antibody (mouse monoclonal) | BioLegend | Cat# 312231, RRID:AB_2734286 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0161 anti-human CD11b antibody (mouse monoclonal) | BioLegend | Cat# 301353, RRID:AB_2734249 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0053 anti-human CD11c antibody (mouse monoclonal) | BioLegend | Cat# 371519, RRID:AB_2749971 | (0.025 µg per million cells) |
| Antibody | TotalSeq-A0064 anti-human CD123 antibody (mouse monoclonal) | BioLegend | Cat# 306037, RRID:AB_2749977 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0390 anti-human CD127 (IL-7Rα) antibody (mouse monoclonal) | BioLegend | Cat# 351352, RRID:AB_2734366 | (0.025 µg per million cells) |
| Antibody | TotalSeq-A0081 anti-human CD14 antibody (mouse monoclonal) | BioLegend | Cat# 301855, RRID:AB_2734254 | (0.2 µg per million cells) |
| Antibody | TotalSeq-A0163 anti-human CD141 (thrombomodulin) antibody (mouse monoclonal) | BioLegend | Cat# 344121, RRID:AB_2783229 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0083 anti-human CD16 antibody (mouse monoclonal) | BioLegend | Cat# 302061, RRID:AB_2734255 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0408 anti-human CD172a (SIRPα) antibody (mouse monoclonal) | BioLegend | Cat# 372109, RRID:AB_2783285 | (0.25 µg per million cells) |
| Antibody | TotalSeq-A0144 anti-human CD185 (CXCR5) antibody (mouse monoclonal) | BioLegend | Cat# 356937, RRID:AB_2750356 | (0.125 µg per million cells) |
| Antibody | TotalSeq-A0050 anti-human CD19 antibody (mouse monoclonal) | BioLegend | Cat# 302259, RRID:AB_2734256 | (0.2 µg per million cells) |
| Antibody | TotalSeq-A0242 anti-human CD192 (CCR2) antibody (mouse monoclonal) | BioLegend | Cat# 357229, RRID:AB_2750501 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0148 anti-human CD197 (CCR7) antibody (mouse monoclonal) | BioLegend | Cat# 353247, RRID:AB_2750357 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0181 anti-human CD21 antibody (mouse monoclonal) | BioLegend | Cat# 354915, RRID:AB_2750006 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0180 anti-human CD24 antibody (mouse monoclonal) | BioLegend | Cat# 311137, RRID:AB_2750374 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0085 anti-human CD25 antibody (mouse monoclonal) | BioLegend | Cat# 302643, RRID:AB_2734258 | (0.08 µg per million cells) |
| Antibody | TotalSeq-A0056 anti-human CD269 (BCMA) antibody (mouse monoclonal) | BioLegend | Cat# 357521, RRID:AB_2749974 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0191 anti-mouse/rat/human CD27 antibody (Armenian hamster monoclonal) | BioLegend | Cat# 124235, RRID:AB_2750344 | (0.125 µg per million cells) |
| Antibody | TotalSeq-A0171 anti-human/mouse/rat CD278 (ICOS) antibody (Armenian hamster monoclonal) | BioLegend | Cat# 313555, RRID:AB_2800824 | (0.01 µg per million cells) |
| Antibody | TotalSeq-A0088 anti-human CD279 (PD-1) antibody (mouse monoclonal) | BioLegend | Cat# 329955, RRID:AB_2734322 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0034 anti-human CD3 antibody (mouse monoclonal) | BioLegend | Cat# 300475, RRID:AB_2734246 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0406 anti-human CD304 (neuropilin-1) antibody | BioLegend | Cat# 354525, RRID:AB_2783261 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0830 anti-human CD319 (CRACC) antibody (mouse monoclonal) | BioLegend | Cat# 331821, RRID:AB_2800872 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0410 anti-human CD38 antibody (mouse monoclonal) | BioLegend | Cat# 356635, RRID:AB_2800967 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0176 anti-human CD39 antibody (mouse monoclonal) | BioLegend | Cat# 328233, RRID:AB_2750005 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0072 anti-human CD4 antibody (mouse monoclonal) | BioLegend | Cat# 300563, RRID:AB_2734247 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0031 anti-human CD40 antibody (mouse monoclonal) | BioLegend | Cat# 334346, RRID:AB_2749968 | (0.25 µg per million cells) |
| Antibody | TotalSeq-A0063 anti-human CD45RA antibody (mouse monoclonal) | BioLegend | Cat# 304157, RRID:AB_2734267 | (0.0625 µg per million cells) |
| Antibody | TotalSeq-A0087 anti-human CD45RO antibody (mouse monoclonal) | BioLegend | Cat# 304255, RRID:AB_2734268 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0047 anti-human CD56 (NCAM) antibody (mouse monoclonal) | BioLegend | Cat# 362557, RRID:AB_2749970 | (0.15 µg per million cells) |
| Antibody | TotalSeq-A0166 anti-human CD66b antibody (mouse monoclonal) | BioLegend | Cat# 392905, RRID:AB_2750372 | (0.25 µg per million cells) |
| Antibody | TotalSeq-A0394 anti-human CD71 antibody (mouse monoclonal) | BioLegend | Cat# 334123, RRID:AB_2800884 | (0.025 µg per million cells) |
| Antibody | TotalSeq-A0005 anti-human CD80 antibody (mouse monoclonal) | BioLegend | Cat# 305239, RRID:AB_2749958 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0006 anti-human CD86 antibody (mouse monoclonal) | BioLegend | Cat# 305443, RRID:AB_2734273 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0080 anti-human CD8a antibody (mouse monoclonal) | BioLegend | Cat# 301067, RRID:AB_2734248 | (0.2 µg per million cells) |
| Antibody | TotalSeq-A0156 anti-human CD95 (Fas) antibody (mouse monoclonal) | BioLegend | Cat# 305649, RRID:AB_2750368 | (0.1 µg per million cells) |
| Antibody | TotalSeq-A0352 anti-human FcεRIα antibody (mouse monoclonal) | BioLegend | Cat# 334641, RRID:AB_2750503 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0159 anti-human HLA-DR antibody (mouse monoclonal) | BioLegend | Cat# 307659, RRID:AB_2750001 | (0.25 µg per million cells) |
| Antibody | TotalSeq-A0384 anti-human IgD antibody (mouse monoclonal) | BioLegend | Cat# 348243, RRID:AB_2783238 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0090 Mouse IgG1, κ isotype Ctrl antibody (mouse monoclonal) | BioLegend | Cat# 400199, RRID:AB_2868412 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0136 anti-human IgM antibody (mouse monoclonal) | BioLegend | Cat# 314541, RRID:AB_2749992 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0153 anti-human KLRG1 (MAFA) antibody (mouse monoclonal) | BioLegend | Cat# 367721, RRID:AB_2750373 | (0.25 µg per million cells) |
| Antibody | TotalSeq-A0584 anti-human TCR Vα24-Jα18 (iNKT cell) antibody (mouse monoclonal) | BioLegend | Cat# 342923, RRID:AB_2783227 | (0.5 µg per million cells) |
| Antibody | TotalSeq-A0581 anti-human TCR Vα7.2 antibody (mouse monoclonal) | BioLegend | Cat# 351733, RRID:AB_2783246 | (0.05 µg per million cells) |
| Antibody | TotalSeq-A0224 anti-human TCR α/β antibody (mouse monoclonal) | BioLegend | Cat# 306737, RRID:AB_2783167 | (0.125 µg per million cells) |
| Antibody | TotalSeq-A0139 anti-human TCR γ/δ antibody (mouse monoclonal) | BioLegend | Cat# 331229, RRID:AB_2734325 | (0.5 µg per million cells) |
| Sequence-based reagent | MOSAIC_Bot | Integrated DNA Technologies | Tn5 complex oligo | 5'-/5phos/CTGTCTCTTATACACATCT-'3; standard desalting |
| Sequence-based reagent | Tn5ME-s7_Top | Integrated DNA Technologies | Tn5 complex oligo | 5'-GTCTCGTGGGCTCGGAGA
TGTGTATAAGAGACAG-3'; standard desalting |
| Sequence-based reagent | Poly-A Top-L | Integrated DNA Technologies | Tn5 complex oligo | 5'-TTTTTTTTTTTTTTT TTTTTTTTTTTTTTT VNAGATGTGTATAAGAGACAG -3'; standard desalting |
| Sequence-based reagent | SI-P5-22 | Integrated DNA Technologies | PCR primer | 5'-AATGATACGGCGACCACCG
AGATCTACACTCTTTCCCTACAC GACGCTCTTCCGATCT-3'; standard desalting |
| Sequence-based reagent | F BC primer | Integrated DNA Technologies | PCR primer | 5'-CTACACGACGCT
CTTCCGATCT-3'; standard desalting |
| Sequence-based reagent | ADT-Rev-AMP | Integrated DNA Technologies | PCR primer | 5'-CCTTGGCACCCGAGAATTCC-3'; standard desalting |
| Sequence-based reagent | TruSeq R1 Seq primer | Integrated DNA Technologies | PCR primer | 5'-ACACTCTTTCCCTACACG
ACGCTCTTCCGATCT-3'; standard desalting |
| Sequence-based reagent | ADT-i7 primer | Integrated DNA Technologies | PCR primer | 5'-CAAGCAGAAGACGGCA
TACGAGATNNNNNNNN GTGACTGGAGTTCCT TGGCACCCGAGAATTCC*A-3'; PAGE purification; * = phosphorothioate bond; N’s indicate barcode position |
| Sequence-based reagent | SI-PCR-Oligo | Integrated DNA Technologies | PCR primer | 5'-AATGATACGGCGACCA
CCGAGATCTACACTCTT TCCCTACACGACGCTC-3'; standard desalting |
| Peptide, recombinant protein | Tn5 transposase | Beta Lifescience | TN5-BL01 | |
| Commercial assay or kit | Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 | 10x Genomics | 1000121 | |
| Commercial assay or kit | Next GEM Chip G Single Cell Kit | 10x Genomics | 1000120 | |
| Commercial assay or kit | Single Index Kit T Set A | 10x Genomics | 1000213 | |
| Commercial assay or kit | Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 | 10x Genomics | 1000175 | |
| Commercial kit or assay | Next GEM Chip H Single Cell Kit | 10x Genomics | 1000161 | |
| Commercial kit or assay | Single Index Kit N Set A | 10x Genomics | 1000212 | |
| Commercial kit or assay | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle | 10x Genomics | 1000283 | |
| Commercial kit or assay | Next GEM Chip J Single Kit | 10x Genomics | 1000234 | |
| Commercial kit or assay | Dual Index Kit TT Set A | 10x Genomics | 1000215 | |
| Commercial kit or assay | Quant-iT PicoGreen dsDNA Assay Kit | Thermo Fisher Scientific | P7589 | |
| Commercial kit or assay | Library Quantification Kit, Illumina Platform | KAPA Biosystems | KK4844 | |
| Commercial kit or assay | Bioanalyzer high-sensitivity DNA analysis | Agilent Technologies | 5067-4626 | |
| Software, algorithm | R | The R Foundation | RRID:SCR_001905 | v3.6.3 and >4.0.2 |
| Software, algorithm | ArchR | Jeffrey Granja and Ryan Corces | v1.0.1 | |
| Software, algorithm | BarCounter | Elliott Swanson; this study | ||
| Software, algorithm | cellranger | 10x Genomics | v5.0.0 | |
| Software, algorithm | cellranger-atac | 10x Genomics | v1.1.0 and v1.2.0 | |
| Software, algorithm | cellranger-arc | 10x Genomics | v1.0.0 | |
| Software, algorithm | Seurat | Paul Hoffman, Satija Lab, and Collaborators | RRID:SCR_016341 | v4.0-beta |
| Software, algorithm | FlowJo | BD | v10.7 | |
| Other | Digitonin | MP Biomedicals | 0215948082 | |
| Other | Human TruStain FcX | BioLegend | 422302 | |
| Other | ViaStain acridine orange/propidium iodide solution | Nexcelom Bioscience | CS2-0106-25mL | |
| Other | Dynabeads MyOne SILANE | Thermo Fisher Scientific | 37002D | |
| Other | Fixable Viability Stain 510 | BD Biosciences | 564406 | |
| Other | IGEPAL-CA630 | Sigma | I8896 | CAS 9002-93-1 |
| Other | SPRIselect | Beckman Coulter | B23319 | |
| Other | NEBNext Ultra II Q5 Master Mix | New England Biolabs | M0544 | |
| Other | KAPA HiFi HotStart ReadyMix | KAPA Biosystems | KM2602 | |
| Other | Protector RNase Inhibitor | Sigma-Aldrich | 03335399001 | |
| Other | Fixable Viability Stain 510 | BD Biosciences | Cat# 564406, RRID:AB_2869572 |