Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Healthy HLA-A02 PBMCs | StemCell Technologies | Cat#70025 |
| Chemicals, peptides, and recombinant proteins | ||
| Biotinylated HLA-A2 MHC-I Monomer | Fred Hutchinson Cancer Research Center Immune Monitoring Shared Resource | N/A |
| NLVPMVATV peptide | IBA-Lifesciences | N/A |
| PE-conjugated streptavidin | Thermo Fisher | Cat#SA10041 |
| APC-conjugated streptavidin | Thermo Fisher | Cat#SA1005 |
| 500 kDa biotin-dextran | Nanocs | Cat#DX500-BN-1 |
| Critical commercial assays | ||
| Single Cell Immune Profiling Kit | 10X | Cat#1000542 |
| Deposited data | ||
| VDJDB | Shugay et al.13 | https://vdjdb.cdr3.net/ |
| TBAdb | Zhang et al.14 | https://db.cngb.org/pird/home/ |
| McPAS-TCR | Tickotsky et al.15 | http://friedmanlab.weizmann.ac.il/McPAS-TCR/ |
| MIRA COVID sequences | Nolan et al.44 | https://doi.org/10.21203/rs.3.rs-51964/v1 |
| Raw and Analyzed Data | This paper | SRA: PRJNA918821 |
| Software and algorithms | ||
| R v4.1.1 | CRAN | https://cran.r-project.org/ |
| RStudio v1.4.1717 | RStudio | https://www.rstudio.com |
| uwot R package | James Melville | https://github.com/jlmelville/uwot |
| data.table R package | Matt Dowle | https://cran.r-project.org/web/packages/data.table/index.html |
| dplyr R package | Hadley Wickham | https://cran.r-project.org/web/packages/dplyr/index.html |
| ggplot2 R package | Thomas Lin Pedersen | https://cran.r-project.org/web/packages/ggplot2/index.html |
| pheatmap R package | Raivo Kolde | https://cran.r-project.org/web/packages/pheatmap/index.html |
| ggnewscale R package | Elio Campitelli | https://cran.r-project.org/web/packages/ggnewscale/index.html |
| GLIPH | Glanville et al.34 | http://50.255.35.37:8080/ |
| AlphaFold v2.0 | Deepmind | https://github.com/deepmind/alphafold |
| SPAN-TCR | This paper | https://doi.org/10.5281/zenodo.7637683 |
| Other | ||
| UV Crosslinker | Boekel | Cat#234100 |