KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD8-BV510 clone SK1 | BioLegend | CAT# 344731 |
| CD14-BV510 clone M5E2 | BioLegend | CAT# 301841 |
| CD19-BV510 clone HIB19 | BioLegend | CAT# 302241 |
| CD56-BV510 clone 5.1H11 | BioLegend | CAT# 362533 |
| CD3-BV421 clone SK7 | BioLegend | CAT# 344833 |
| CD69-BV650 clone FN50 | BioLegend | CAT# 310933 |
| CD154-PE clone 24-31 | BioLegend | CAT# 310805 |
| CD45RO-APC/Fire750 clone UCHL1 | BioLegend | CAT# 304249 |
| TotalSeq-C IL7RA clone A019D5 | BioLegend | CAT# 351356 |
| TotalSeq-C CCR7 clone G043H7 | BioLegend | CAT# 353251 |
| TotalSeq-C CD25 clone BC96 | BioLegend | CAT# 302649 |
| TotalSeq-C CD27 clone O323 | BioLegend | CAT# 302853 |
| TotalSeq-C CD3 clone UCHT1 | BioLegend | CAT# 300479 |
| TotalSeq-C CD4 clone RPA-T4 | BioLegend | CAT# 300567 |
| TotalSeq-C CD8 clone RPA-T8 | BioLegend | CAT# 301071 |
| TotalSeq-C CD45RA clone HI100 | BioLegend | CAT# 304163 |
| TotalSeq-C CD45RO clone UCHL1 | BioLegend | CAT# 304259 |
| TotalSeq-C CD62L clone DREG-56 | BioLegend | CAT# 304851 |
| TotalSeq-C CD69 clone FN50 | BioLegend | CAT# 310951 |
| TotalSeq-C HLA-DR clone L243 | BioLegend | CAT# 307663 |
| TotalSeq-C CD47 clone CC2C6 | BioLegend | CAT# 323131 |
| TotalSeq-C CCR5 clone J418F1 | BioLegend | CAT# 359137 |
| TotalSeq-C CXCR3 clone G025H7 | BioLegend | CAT# 353747 |
| TotalSeq-C CCR6 clone G034E3 | BioLegend | CAT# 353440 |
| TotalSeq-C CCR4 clone L291H4 | BioLegend | CAT# 359425 |
| TotalSeq-C CXCR5 clone J252D4 | BioLegend | CAT# 356939 |
| TotalSeq-C CD40L clone 24-31 | BioLegend | CAT# 310849 |
| TotalSeq-C 4-1BB clone 4B4-1 | BioLegend | CAT# 309839 |
| TotalSeq-C OX40 clone ACT35 | BioLegend | CAT# 350035 |
| TotalSeq-C PD-1 clone EH12.2H7 | BioLegend | CAT# 329963 |
| TotalSeq-C CTLA-4 clone BNI3 | BioLegend | CAT# 369621 |
| TotalSeq-C TIGIT clone A15153G | BioLegend | CAT# 372729 |
| TotalSeq-C mouse IgG1 clone MOPC-21 | BioLegend | CAT# 400187 |
| TotalSeq-C mouse IgG2a clone MOPC-173 | BioLegend | CAT# 400293 |
| TotalSeq-C mouse IgG2b clone MPC-11 | BioLegend | CAT# 400381 |
| TotalSeq-C human hashing antibody 1 | BioLegend | CAT# 394661 |
| TotalSeq-C human hashing antibody 2 | BioLegend | CAT# 394663 |
| TotalSeq-C human hashing antibody 3 | BioLegend | CAT# 394665 |
| TotalSeq-C human hashing antibody 4 | BioLegend | CAT# 394667 |
| TotalSeq-C human hashing antibody 5 | BioLegend | CAT# 394669 |
| TotalSeq-C human hashing antibody 6 | BioLegend | CAT# 394671 |
| TotalSeq-C human hashing antibody 7 | BioLegend | CAT# 394673 |
| TotalSeq-C human hashing antibody 8 | BioLegend | CAT# 394675 |
| TotalSeq-C human hashing antibody 9 | BioLegend | CAT# 394677 |
| TotalSeq-C human hashing antibody 10 | BioLegend | CAT# 394679 |
| CD45RA-BUV737 clone HI100 | BD Biosciences | CAT# 612846 |
| CCR7-BUV395 clone 3D12 | BD Biosciences | CAT# 740267 |
| CTLA4-PE-Dazzel594 clone L3D10 | Bioledgend | CAT# 349921 |
| IFNG-BV711 clone 4S.B3 | BD Biosciences | CAT# 564793 |
| TNF-BV605 clone Mab11 | Biolegend | CAT# 502935 |
| p24-PE clone KC57 | Beckman Coulter | CAT# 6604667 |
| p24-APC clone 28B7 | Medimabs | CAT# MM-0289-APC |
| GZMB-AF700 GB11 | BD Biosciences | CAT# 561016 |
| Biological samples | ||
| Demographics of study participants, see Table S1 | This paper | N/A |
| Human serum | Sigma Aldrich | CAT# H4522-20ML |
| Chemicals, peptides, and recombinant proteins | ||
| Staphylococcal enterotoxin type B (SEB) toxin | List Biological Laboratories | CAT# 122 |
| HIV-1 group B Gag, Pol, Env, and Nef peptide pools | NIH HIV Reagent Program | CAT# 12425, 12438, 12540, 12545 |
| CMV lysate, strain AD-169 | ZeptoMetrix | CAT# 810003 |
| HCMV pp65 peptide pool | NIH HIV Reagent Program | CAT# 11549 |
| enfuvirtide | NIH HIV Reagent Program | CAT# 12732 |
| Ionomycin | Millipore | CAT# 407950-1MG |
| PMA | Millipore | CAT# 5.00582.0001 |
| Brefeldin A | Thermo Fisher Scientific | CAT# 00-4506-51 |
| Monensin | Thermo Fisher Scientific | CAT# 00-4505-51 |
| CD40 antibody | Miltenyi Biotech | CAT# 130-094-133 |
| Critical commercial assays | ||
| Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 | 10x Genomics | PN-1000165 |
| Chromium Single Cell V(D)J Enrichment Kit, Human T Cell | 10x Genomics | PN-1000005 |
| Chromium Single Cell 5’ Feature Barcode Library Kit | 10x Genomics | PN-1000080 |
| NEBNext Immune Sequencing Kit | New England Biolabs | CAT# E6320S |
| EasySep Direct Human CD4+ T cell kit | STEMCELL | 19662 |
| CD4 T cell isolation kit, human | Miltenyi Biotech | 130-096-533 |
| EasySep Dead Cell Removal (Annexin V) Kit | STEMCELL | 17899 |
| Dynabead CD8 | Thermo Fisher | 11147D |
| LIVE/DEAD Fixable Aqua Dead Cell Stain Kit | Thermo Fisher | L34957 |
| LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit | Thermo Fisher | L10119 |
| Deposited data | ||
| ECCITE-seq unstimulated CD4+ T cells | This study | GSE187515 |
| ECCITE-seq stimulated CD4+ T cells | This study | GSE187515 |
| Bulk TCR repertoire profiling from HIV-1 infected and uninfected individuals | This study | GSE187515 |
| Software and algorithms | ||
| cellranger count version 3.0.2 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/3.0/ |
| cellranger vdj version 3.1 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/3.1/ |
| Seurat version 4.0.3 | Stuart et al. 2018 | https://cran.r-project.org/web/packages/Seurat/index.html |
| batchelor version 1.6.3 | Haghverdi et al., 2018 | https://www.bioconductor.org/packages/release/bioc/html/batchelor.html |
| uwot version 0.1.10 | NA | https://cran.r-project.org/web/packages/uwot/index.html |
| STAR version 2.5.3 | Dobin et al., 2012 | https://github.com/alexdobin/STAR |
| WGCNA version 1.70-3 | Langfelder and Horvath, 2008 | https://cran.r-project.org/web/packages/WGCNA/index.html |
| pRESTO version 0.6.1 | Vander Heiden et al., 2014 | https://presto.readthedocs.io/en/stable/ |
| ChangeO version 1.0.0 | Gupta et al., 2015 | https://changeo.readthedocs.io/en/stable/ |
| scikit-learn version 0.23 | Pedregosa et al., 2011) | https://scikit-learn.org/stable/ |
| IPA summer 2021 release | Krämer et al., 2014 | https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/ |
| scRFE, version 1.5.6 | Park et al., 2020) | https://github.com/czbiohub/scRFE |
| Imbalanced-learn version 0.7.0 | Lemaître et al., 2017 | https://imbalanced-learn.org/stable/ |
| fGSEA version 1.16.0 | Korotkevich et al., 2019) | http://bioconductor.org/packages/release/bioc/html/fgsea.html |
| R version 4.0.3 | R Core Team (2021) | https://www.r-project.org/ |
| CodonCode version 7 | CodonCode Corporation | https://www.codoncode.com/aligner/ |
| Analysis scripts | This paper | https://github.com/Ya-ChiHo/Collora-and-Liu-et-al-2022 |