KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-human CD45RO | Biolegend | Cat# 304238; RRID:AB_2562153 or Cat# 304233; RRID:AB_11219394 |
| Mouse anti-human CD197 (CCR7) | Biolegend | Cat# 353234; RRID:AB_2563867 or Cat# 353208; RRID:AB_11203894 |
| Mouse anti-human CD4 | Biolegend | Cat# 344634; RRID:AB_2566017 or Cat# 317408; RRID:AB_571951 |
| Mouse anti-human CD3 | Biolegend | Cat# 300472; RRID:AB_2687178 |
| Armenian hamster anti-human/mouse/rat CD278 (ICOS) | Biolegend | Cat# 313528; RRID:AB_2566126 |
| Mouse anti-human CD38 | Biolegend | Cat# 303508; RRID:AB_314360 |
| Mouse anti-human CD11b | Biolegend | Cat# 301342; RRID:AB_2563395 or Cat# 301308; RRID:AB_314160 |
| Mouse anti-human CD19 | Biolegend | Cat# 302210; RRID:AB_314240 or Cat# 302218; RRID:AB_314248 |
| Mouse anti-human CD25 antibody | Biolegend | Cat# 302630; RRID:AB_11126749 |
| Mouse anti-human CD127 antibody | Biolegend | Cat# 351322; RRID:AB_10897104 |
| Mouse anti-human IFN-γ antibody | Biolegend | Cat# 502506; RRID:AB_315231 |
| Mouse anti-human TNF-α antibody | Biolegend | Cat# 502928; RRID:AB_2561315 |
| Rat anti-hunab IL-2 antibody | Biolegend | Cat# 500338; RRID:AB_2562632 |
| Rat anti-human Foxp3 antibody | ThermoFisher | Cat# 56-4776-41; RRID:AB_1582210 |
| Biotin-conjugated 4G2 monoclonal antibody | ATCC | Cat# HB-112; RRID:CVCL_J890 |
| Bacterial and Virus Strains | ||
| YFV-17D | BEI Resources | NR-115 |
| Biological Samples | ||
| Healthy Adult Human Peripheral Blood Sample | Hospital of the University of Pennsylvania | https://www.pennmedicine.org/ |
| Pre-Immune Yellow Fever Virus Serum | BEI Resources | Cat# NR-42565 |
| Early-Immune Yellow Fever Virus Antiserum (Polyclonal Antiserum) | BEI Resources | Cat# NR-29337 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| LIVE/DEAD™ Fixable Dead Cell Stain Kits | Invitrogen | Cat# L34966 or Cat# L34976 |
| CellTrace™ Violet Cell Proliferation Kit | ThermoFisher | Cat# C34557 |
| Recombinant Human IL-2 | Peprotech | Cat# 200-02 |
| Recombinant Human IL-7 | Peprotech | Cat# 200-07 |
| Recombinant Human IL-15 | Peprotech | Cat# 200-15 |
| Recombinant Human GM-CSF (carrier-free) | Biolegend | Cat# 572904 |
| Recombinant Human IL-4 (carrier-free) | Biolegend | Cat# 574006 |
| YF23 (NS3 313 - 327); Seq: ESATILMTATPPGTS | This paper | N/A |
| YF25 (NS3 448 - 462); Seq: KGPLRISASSAAQRR | This paper | N/A |
| YF31 (NS4b 37 - 51); Seq: GAAWTVYVGIVTMLS | This paper | N/A |
| YF38 (NS5 398 - 412); Seq: EEFIAKVRSHAAIGA | This paper | N/A |
| YF42 (NS5 756 - 770); Seq: ACLSKAYANMWSLMY | This paper | N/A |
| YF44 (NS5 867 - 881); Seq: IHLVIHRIRTLIGQE | This paper | N/A |
| YF45 (NS3 147 - 161); Seq: GEVIGLYGNGILVGD | This paper | N/A |
| YF48 (EE 43 - 59); Seq: ISLETVAIDRPAEVRKV | This paper | N/A |
| YF50 (EE 241 - 257); Seq: TIRVLALGNQEGSLKTA | This paper | N/A |
| YF51 (EE 301 - 317); Seq: TDKMFFVKNPTDTGHGT | This paper | N/A |
| YF53 (NS3 151 - 167); Seq: GLYGNGILVGDNSFVSA | This paper | N/A |
| YF54 (NS3 367 - 383); Seq: LPSIRAANVMAASLRKA | This paper | N/A |
| YF57 (NS5 7 - 23); Seq: TLGEVWKRELNLLDKRQ | This paper | N/A |
| YF69 (NS3 355 - 371); Seq: WILADKRPTAWFLPSIR | This paper | N/A |
| YF80 (EE 313 - 329); Seq: TGHGTVVMQVKVSKGAP | This paper | N/A |
| YF81 (NS3 283 - 299); Seq: WEVIIMDEAHFLDPASI | This paper | N/A |
| YF91 (NS5 367 - 383); Seq: PPAGTRKIMKVVNRWLF | This paper | N/A |
| YF93 (EE 457 - 473); Seq: MGAVLIWVGINTRNMTM | This paper | N/A |
| YF108 (NS5 325 - 341); Seq: VIKILTYPWDRIEEVTR | This paper | N/A |
| YF111 (NS5 619 - 635); Seq: VQLIRMAEAEMVIHHQH | This paper | N/A |
| HA306; Seq: GGPKYVKQNTLKLAT | This paper | N/A |
| CLIP103; Seq: CGGGPVSKMRMATPLLMQA | This paper | N/A |
| TT511; Seq: CGGKIIVDYNLQSK | This paper | N/A |
| Ni-NTA Agarose | QIAGEN | Cat# 30230 |
| Methyl Cellulose | Sigma-Aldrich | Cat# M0512-250G |
| Amphotericin B | Gibco | Cat# 15290-018 |
| TrueBlue peroxidase substrate | KPL | Cat# 5510-0030 |
| AccuCount Fluorescent Particles | Spherotech | Cat# ACFP-50-5 |
| Horseradish peroxidase (HRP)-conjugated streptavidin | BD Biosciences | Cat# 554066 |
| HRP | MP Biomedicals | Cat# ICN55563 |
| BSA | Sigma-Aldrich | Cat# A8022-500G |
| PFA | Electron Microscopy Sciences | Cat# 15714-S |
| Triton-X | Roche | Cat# 10789704001 |
| TBS 10X | Thermo Scientific Pierce | Cat# 37520 |
| Tween | Fisher Bioreagent | Cat# BP337100 |
| HEPES | Corning | Cat# 25-060-Cl |
| L-glut | Mediatech | Cat# MT25-0050CI |
| NaHCO3 | Sigma-Aldrich | Cat# S4019-500G |
| Phorbol myristate acetate (PMA) | Sigma-Aldrich | Cat# P8139-5MG |
| Ionomycin calcium salt from Streptomyces conglobatus | Sigma-Aldrich | Cat# I0634-5MG |
| Brefeldin A | Sigma-Aldrich | Cat# B7651-5MG |
| Monensin | Biolegend | Cat# 420701 |
| Lipopolysaccharides | Sigma-Aldrich | Cat# L4391 |
| ESF 921 Insect Cell Culture Medium | Expression System | Cat# 96-001-01 |
| Critical Commercial Assays | ||
| RosetteSep™ Human Monocyte Enrichment Cocktail | STEMCELL | Cat# 15068 |
| RosetteSep™ Human CD4+ T Cell Enrichment Cocktail | STEMCELL | Cat# 15062 |
| RosetteSep™ Human T Cell Enrichment Cocktail | STEMCELL | Cat# 15061 |
| HotStarTaq DNA polymerase kit | Qiagen | Cat# 203205 |
| NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles) | Illumina | Cat# 20024905 |
| CellsDirect™ One-Step qRT-PCR Kit | Invitrogen™ | Cat# 11753-500 |
| MinElute Gel Extraction Kit | Qiagen | Cat# 28604 |
| BD Cytofix/Cytoperm™ Fixation/Permeablization Kit | BDBioscience | Cat# 554714 |
| eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | ThermoFisher | Cat# 00-5523-00 |
| Deposited Data | ||
| Yellow fever virus-specific TCR sequencing data | This paper | Mendeley Data, V1, doi:10.17632/75xhmfrpm6.1 |
| Experimental Models: Cell Lines | ||
| Hi5 insect cells | ThermoFisher | Cat# B85502 |
| Vero cells | ATCC | CCL-81 |
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and Algorithms | ||
| FlowJo (Version: 10.6.0) | Tree Star | https://www.flowjo.com/ |
| GraphPad Prism 6 | GraphPad | https://www.graphpad.com/ |
| R Version 3.6.3 | R Foundation for Statistical Computing | https://www.r-project.org/ |
| RStudio Version 1.3.959 | R studio | https://www.rstudio.com/ |
| Bcl2fastq | Illumina | https://support.illumina.com/ |
| Pandaseq | Masella, A., et al. (2012). PANDAseq: paired-end assembler for illumina sequences. BMC bioinformatics. DOI: 10.1186/1471-2105-13-31 | https://github.com/neufeld/pandaseq |
| MiXCR | Bolotin, D., et al. (2015). MiXCR: software for comprehensive adaptive immunity profiling. Nature methods. DOI: 10.1186/1471-2105-13-31 | https://github.com/milaboratory/mixcr |
| Circlize Version:0.4.11 | Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics. DOI:10.1093/bioinformatics/btu393 | https://CRAN.R-project.org/package=circlize |
| Other | ||
| LS Column | Miltenyi Biotec | Cat# 130-042-401 |
| Superdex® 200 Increase 10/300 GL | Sigma | Cat# GE28-9909-44 |
| Graphical abstract | This paper | BioRender |