KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet 605 CD25, clone BC96 | Biolegend | Cat# 302632 |
| Brilliant Violet 786 CD127, clone A019D5 | Biolegend | Cat# 351330 |
| Brilliant Violet 421 CD4, clone OKT4 | Biolegend | Cat# 317434 |
| Brilliant Violet 650 CD3, clone UCHT1 | Biolegend | Cat# 300468 |
| Brilliant Ultraviolet 395 CD45, clone H130 | Becton Dickinson | Cat# 563792 |
| Alexa Fluor 647 CD8, clone SK1 | Biolegend | Cat# 344726 |
| FITC GZMK, clone GM26E7 | Biolegend | Cat# 370508 |
| PerCP-Cy5.5 HLA-DR, clone L243 | Biolegend | Cat# 307630 |
| APC-R700 CCR7, clone 3D12 | Becton Dickinson | Cat# 565867 |
| Brilliant Violet 480 CD3, clone UCHT1 | Becton Dickinson | Cat# 566105 |
| Brilliant Violet 510 GZMB, clone GB11 | Becton Dickinson | Cat# 563388 |
| Brilliant Violet 605 Ki67, clone Ki-67 | Biolegend | Cat# 350522 |
| Brilliant Violet 650 CD45RA, clone HI100 | Biolegend | Cat# 304136 |
| Brilliant Violet 786 CD25, clone BC96 | Biolegend | Cat# 302638 |
| Brilliant violet 711 TNFSRF18, clone 108–17 | Biolegend | Cat# 371212 |
| Brilliant ultraviolet 395 CD4, clone RPA-T4 | Becton Dickinson | Cat# 564724 |
| Brilliant ultraviolet 496 CD8, clone RPA-T8 | Becton Dickinson | Cat# 564808 |
| Brilliant ultraviolet 805 CD45, clone HI30 | Becton Dickinson | Cat# 564914 |
| PE-CF594 FoxP3, clone 259D/C7 | Becton Dickinson | Cat# 562421 |
| PE-Cy7 Perforin, clone B-D48 | Biolegend | Cat# 353316 |
| Alexa Fluor 647 IFNγ, clone 4S.B3 | Biolegend | Cat# 502516 |
| PE anti-human TNFα, clone Mab11 | Biolegend | Cat# 502909 |
| CD4, clone SP35 | Cell Marque | Cat# 104R-18 |
| Alexa Fluor 555 goat anti-rabbit IgG(H+L) | Invitrogen | Cat# 4050–32 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Liberase TL, research grade | Millipore Sigma | Cat# 5401020001 |
| Draq7 | Biolegend | Cat# 424001 |
| Live/dead fixable Near-IR dead cell stain | Invitrogen | Cat# L34975 |
| FluoroFix buffer | Biolegend | Cat# 422101 |
| Recombinant human IL-2 | Peprotech | Cat# 200–02 |
| IncuCyte Annexin V Red reagent | Essen Bioscience | Cat# 4641 |
| IncuCyte Cytotox Red reagent | Essen Bioscience | Cat# 4632 |
| RNAscope probe, Homo sapiens, GZMB (channel 2) | Advanced Cell Diagnostics | Cat# 445971-C2 |
| RNAscope probe, Homo sapiens, GZMK (channel 1) | Advanced Cell Diagnostics | Cat# 475901-C1 |
| L15 media, 15 mM HEPES, 600 mg% glucose | UCSF Cell Culture Facility | N/A |
| Fetal bovine serum | Omega Scientific | Cat# FB-01 |
| RPMI-1640 | UCSF Cell Culture Facility | N/A |
| ImmunoCult XF complete medium (Medium + 10% FCS + 1% penicillin / streptomycin) | STEMCELL Technologies | Cat# 10981 |
| Critical Commercial Assays | ||
| GentleMACS | Miltenyi Biotec | Cat# 130-093-235 |
| FoxP3/transcription factor staining buffer set | eBioscience | Cat# 00-5523-00 |
| Cell stimulation cocktail | eBioscience | Cat# 00–4975 |
| Chromium™ Single Cell 3’ Library, Gel Bead & Multiplex Kit | 10X Genomics | Cat# 120233 (discontinued) |
| Chromium™ Single Cell 3’ Chip Kit | 10X Genomics | Cat# 120232 (discontinued) |
| Dynabeads Human T-Activator CD3/CD28/CD137 | Gibco | Cat# 11162D |
| Opal 7-color manual IHC kit | Perkin Elmer | Cat# NEL811001KT |
| Deposited Data | ||
| Processed data | This study | NCBI GEO: GSE149652 |
| Healthy human donor TCR data for CD4+ peripheral blood mononuclear cells | 10X Genomics | https://support.10xgenomics.com/single-cell-vdj/datasets/2.2.0/vdj_v1_hs_cd4_t |
| Healthy human donor TCR data for CD8+ peripheral blood mononuclear cells | 10X Genomics | https://support.10xgenomics.com/single-cell-vdj/datasets/2.2.0/vdj_v1_hs_cd8_t |
| Human reference genome, build hg19 | 10X Genomics | https://software.10xgenomics.com |
| Oligonucleotides | ||
| TCR sequencing primers | Table S3 | N/A |
| Software and Algorithms | ||
| Cell Ranger v1.1 | 10X Genomics | https://software.10xgenomics.com |
| Scanpy v1.4.3 | Wolf et al., 2018 | https://scanpy.readthedocs.io/en/stable/index.html |
| miXCR v2.1.12 | Bolotin et al., 2015 | https://mixcr.readthedocs.io/en/latest/ |
| Monocle v2.10.1 | Qiu et al., 2017 | Bioconductor |
| SingleR v1.1.9 | Aran et al., 2019 | Bioconductor |
| FlowJo | TreeStar | N/A |