KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| p24 KC57-PE | Beckman Coulter | Cat#6604667 |
| p24 28B7-APC | MediMabs | Cat#MM-0289-APC |
| CD4-APC-H7 (Clone: RPA-T4) | BD Bioscience | Cat#560168 |
| CD45RA-A700 (Clone: HI100) | BD Bioscience | Cat#560673 |
| CXCR5-BB515 (Clone: RF8B2) | BD Bioscience | Cat#564624 |
| CXCR3-PerCP-Cy5.5 (Clone: 1C6/CXCR3) | BD Bioscience | Cat#560832 |
| Ki67-PE-Cy7 (Clone: B56) | BD Bioscience | Cat#561283 |
| CCR5-BV421 (Clone: 2D7/CCR5) | BD Bioscience | Cat#562576 |
| CD45RA-BV786 (Clone: HI100) | BD Bioscience | Cat#563870 |
| HLA-DR-BV605 (Clone: G46-6) | BD Bioscience | Cat#562845 |
| CCR7-BB515 (Clone: 3D12) | BD Bioscience | Cat#565870 |
| PD-1-BV605 (Clone: EH12.2H7) | BioLegend | Cat#329923 |
| ICOS-BV785 (Clone: C398.4a) | BioLegend | Cat#313534 |
| HLA-ABC-A700 (Clone: W6/32) | BioLegend | Cat#311437 |
| CD69-PerCP-Cy5.5 (Clone: FN50) | BioLegend | Cat#310926 |
| Bcl-2-BV421 (Clone: 100) | BioLegend | Cat#658709 |
| Live/Dead Aqua Cell Stain (405nm) | ThermoFisher Scientific | Cat#L34957 |
| Biological samples | ||
| Human serum | Atlanta Biologicals | Cat#540110 |
| Demographics of study participants, see Table S1 | This paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Lamivudine (3TC) | NIH HIV Reagent Program | ARP-8146 |
| Raltegravir (RAL) | NIH HIV Reagent Program | HRP-11680 |
| Brefeldin A (BFA) | Sigma | Cat#B2651 |
| ionomycin | Sigma | Cat#I9657 |
| PMA | Sigma | Cat#P8139 |
| DirectPCR Lysis Reagent | Viagen Biotech | Cat#301-C |
| Proteinase K | Wisent | Cat#25530–015 |
| Proteinase K | Invitrogen | Cat#25530-015, |
| Critical commercial assays | ||
| EasySep Human CD4+ T Cell Enrichment Kit | StemCell Technology | Cat#19052 |
| FoxP3 Transcription Factor Staining Buffer Set | eBioscience | Cat#00-5523-00 |
| Phusion Master Mix | ThermoFisher Scientific | Cat#F531S |
| Taq DNA Polymerase kit | Invitrogen | Cat#18038-042, |
| Qiagen Multiplex PCR kit | Qiagen | Cat#206143 |
| QIAquick 96 PCR Purification kit | Qiagen | Cat#28181 |
| Platinum SuperFi II Master Mix | Life Tech | Cat#12368010 |
| AMPure XP | Beckman Coulter | Cat#A63881 |
| Deposited data | ||
| HIV env | GenBank | Genbank accession numbers ON500682 to ON500846 |
| HIV near full length sequences | GenBank | Genbank accession numbers ON500847 to ON501069 |
| TCRβ sequences | This paper | N/A |
| Oligonucleotides | ||
| TCRβ HIV env and HIV near full length amplification and sequencing primers, see Table S2 | This paper | N/A |
| Software and algorithms | ||
| MiXCR version 3.0.13 | Bolotin et al.29 | https://github.com/milaboratory/mixcr |
| IMGT® database | IMGT®, the international ImMunoGeneTics information system® | http://www.imgt.org |
| McPAS-TCR database | Friedman lab | http://friedmanlab.weizmann.ac.il/McPAS-TCR/ |
| Prism version 9.1.0 | Graphpad | https://www.graphpad.com |
| FlowJo version 10.7.1 | FlowJo | https://www.flowjo.com/solutions/flowjo |
| iqtree2, version 2.1.2 | IQTREE | http://www.iqtree.org |
| FigTree version 1.4.4 | Figtree | http://tree.bio.ed.ac.uk/software/figtree/ |
| HIVDatabase QCTool | HIV Los Alamos | https://www.hiv.lanl.gov/content/sequence/QC/index.html |
| ProseqIT | NIH | https://psd.cancer.gov/tools/nvs_annot.php |
| GeneCutter tool | HIV Los Alamos | https://www.hiv.lanl.gov/content/sequence/GENE_CUTTER/cutter.html |