| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| IgG mouse anti-human (PE, clone JDC-10) | SouthernBiotech | 9040–09; RRID:AB_2796601 |
| IgG1 mouse anti-human (PE, clone HP6001) | SouthernBiotech | 9054–09; RRID:AB_2796628 |
| IgG2 mouse anti-human (PE, clone HP6025) | SouthernBiotech | 9070–09; RRID:AB_2796639 |
| IgG3 mouse anti-human (PE, clone HP6050) | SouthernBiotech | 9210–09; RRID:AB_2796701 |
| IgG4 mouse anti-human (PE, clone HP6025) | SouthernBiotech | 9200–09; RRID:AB_2796693 |
| IgE mouse anti-human (PE, BE5) | Thermo Fisher | MA1-10375; RRID:AB_2536764 |
| Anti-Human CD45 (CyTOF, 89Y, clone HI30) | Fluidigm | 3089003B; RRID: AB_2661851 |
| Anti-Human CD3 (CyTOF, 115In, clone UCHT1) | Biolegend | 300443; RRID:AB_2562808 |
| Anti-Human CD19 (CyTOF, 142ND, clone HIB19) | Fluidigm | 3142001B; RRID: AB_2651155 |
| Anti-Human CD38 (CyTOF, 144ND, clone HIT2) | Fluidigm | 3144014B; RRID: AB_2687640 |
| Anti-Human CD4 (CyTOF, 145ND, clone RPA-T4) | Fluidigm | 3145001B; RRID: AB_2661789 |
| Anti-Human CD20 (CyTOF, clone 2H7) | Biolegend | 302302; RRID:AB_314250 |
| Anti-Human CD123 (CyTOF, 151Eu, clone 6H6) | Fluidigm | 3151001B; RRID: AB_2661794 |
| Anti-Human CD45RA (CyTOF, 155Gd, clone HI100) | Fluidigm | 3155011B; RRID: AB_2810246 |
| Anti-Human CD1c (CyTOF, 160Gd, clone L161) | Biolegend | 331502;RRID:AB_1088996 |
| Anti-Human CD33 (CyTOF, 163Dy, clone WM53) | Fluidigm | 3163023B; RRID: AB_2687857 |
| Anti-Human CCR7 (CyTOF, 167Er, clone G043H7) | Fluidigm | 3167009A; RRID: AB_2858236 |
| Anti-Human CD25 (CyTOF, 169Tm, clone M-A251) | Fluidigm | 3169003B; RRID: AB_2661806 |
| Anti-Human CD8a (CyTOF, 172Yb, clone RPA-T8) | Biolegend | 301002; RRID:AB_314120 |
| Anti-Human CD14 (CyTOF, 173Yb, clone 61D3) | Thermo Fisher | 14-0149-82; RRID:AB_467129 |
| Anti-Human HLA-DR (CyTOF, 174Yb, clone L243) | Fluidigm | 3174001B; RRID: AB_2665397 |
| Anti-Human CD56 (CyTOF, 176Yb, clone CMSSB) | Fluidigm | 3176003B; RRID: AB_2756430 |
| Anti-Human CD16 (CyTOF, 209Bi, clone 3G8) | Fluidigm | 3209002B; RRID: AB_2756431 |
| Biological samples | ||
| PBMC and Plasma | LJI Clinical Core | https://www.lji.org/research/research-services/clinical-studies/ |
| Chemicals, peptides, and recombinant proteins | ||
| Pertussis Toxin (PT) | List Biologicals | 180 |
| Tetanus Toxoid (TT) | List Biologicals | 191A |
| Pertactin (PRN) | List Biologicals | 187 |
| Fimbriae 2/3 (Fim2/3) | List Biologicals | 186 |
| Diphtheria Toxoid (DT) | List Biologicals | 151 |
| Filamentous Hemagglutinin (FHA) | Sigma | F5551-50UG |
| Ovalbumin (OVA) | Sigma | vac-stova |
| MagPlex-C Microspheres | Luminex | MC10012-01 MC10019-01 MC10025-01 MC10034-01 MC10037-01 MC10042-01 MC10048-01 |
| Zeba TM Spin Desalting Columns 7K MWCO | Thermo Scientific | 89882 |
| Ficoll-Paque PLUS | GE | 17144003 |
| RPMI 1640 medium | Omega Scientific | RP-21 |
| DMSO | Sigma | D8418 |
| QIAzol Lysis Reagent | Qiagen | 79306 |
| Human Pertussis antiserum | NIBSC | 06/140 |
| Cell-ID Intercalator-Ir | Fluidigm | NC1038184 |
| Critical commercial assays | ||
| Target 96 Immuno-oncology panel | Olink | https://olink.com/products-services/target/immune-response-panel/ |
| Target 96 Immune response panel | Olink | https://olink.com/products-services/target/immune-response-panel/ |
| Target 96 Metabolism panel | Olink | https://olink.com/products-services/target/biological-process/ |
| xMAP® Antibody Coupling Kit | Luminex | 40–50016 |
| MAGPIX Calibration Kit | Luminex | MPX-CAL K25 |
| MAGPIX Performance Verification Kit | Luminex | MPX-PVER-K25 |
| miRNeasy Mini Kit | Qiagen | 217084 |
| TruSeq Stranded mRNA Library Prep Kit | Illumina | 20020595 |
| Deposited data | ||
| bulkRNAseq, PBMC subset frequencies, plasma antibody measurements, plasma cytokine measurements. | This paper | https://www.cmi-pb.org/data; https://doi.org/10.5281/zenodo.10789473 |
| Software and algorithms | ||
| R (V4.0.1 - V4.3.1) | R Core Team (2020) | https://www.r-project.org/ |
| FlowJo software version 10.7.0 | BD Biosciences | https://www.flowjo.com/ |
| Python (v3.7+) | Python community | https://www.python.org/ |
| PostgreSQL (V4) | PostgreSQL Team | https://www.postgresql.org/ |
| JIVE | Lock et al.44 | https://cran.r-project.org/web/packages/r.jive/index.html |
| Multiple co-inertia analysis (MCIA) | Meng et al.46 | https://bioconductor.org/packages/release/bioc/html/omicade4.html |
| GLMNET | https://cran.r-project.org/web/packages/glmnet/index.html | |
| STAR (v2.6.1) | Dobin et al.56 | https://github.com/alexdobin/STAR |
| PRINSEQ Lite (v0.20.3) | Schmieder & Edwards57 | https://github.com/uwb-linux/prinseq |
| SAMtools | Li et al.58 | https://github.com/samtools/samtools |
| featureCounts (v1.6.5) | Liao et al.59 | https://subread.sourceforge.net/ |
| Antibody titer data normalization | This paper | https://doi.org/10.5281/zenodo.10642095 |
| Generation computable matrices and MCIA model | This paper | https://doi.org/10.5281/zenodo.10642081 |
| 24 models derived using the literature-based survey | This paper | https://doi.org/10.5281/zenodo.10642079 |
| JIVE models | This paper | https://doi.org/10.5281/zenodo.10642104 |
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