KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor (AF)-conjugated donkey polyclonal anti-rabbit IgG | Thermo Fisher Scientific | catalog no. R37118 RRID:AB_2556546 |
| AF647–conjugated goat polyclonal anti-rabbit IgG | Cell Signaling | catalog no. 4414S RRID:AB_10693544 |
| AF700-conjugated anti-CD44 (IM7) | BD Pharmingen | catalog no. 560568 RRID:AB_1727481 |
| APC-conjugated anti-PD-1 (29F.1A12) | Biolegend | catalog no. 135209 RRID:AB_2251944 |
| APC-Cy7-conjugated anti-CD8a (53-6.7) | BD Biosciences | catalog no. 557654 RRID:AB_396769 |
| BV421 - conjugated anti-CXCR5/CD185 (L138D7) | Biolegend | catalog no. 145512 RRID:AB_2562128 |
| BV711- conjugated anti-CXCR5/CD185 (L138D7) | Biolegend | catalog no. 145529 RRID:AB_2734207 |
| Biotinylated anti-CD3e (145-2C11) | Biolegend | catalog no. 100304 RRID:AB_312669 |
| PE-conjugated anti-GL7 Antigen (GL7) | Biolegend | catalog no. 144608 RRID:AB_2562926 |
| PerCP-Cy5.5-conjugated anti-CD4 (GK1.5) | Biolegend | catalog no. 100434 RRID:AB_893324 |
| BUV395-conjugated anti-CD4 (GK1.5) | BD Biosciences | catalog no. 563790 RRID:AB_2738426 |
| PerCP-Cy5.5-conjugated anti-CD45.1 (A20) | Biolegend | catalog no. 110728 RRID:AB_893345 |
| AF700-conjugated anti-CD45.2 (104) | Biolegend | catalog no. 109822 RRID:AB_493731 |
| PerCP-Cy5.5-conjugated anti-Ki67 (B56) | BD Biosciences | catalog no. 561284 RRID:AB_10611574 |
| PE-Cy7-conjugated anti-PD-1 (29F.1A12) | Biolegend | catalog no. 135216 RRID:AB_10689635 |
| PE-Cy7-conjugated anti-Fas/CD95 (Jo2) | BD Biosciences | catalog no. 557653 RRID:AB_396768 |
| APC-Cy7-conjugated anti-B220 (RA3-6B2) | Biolegend | catalog no. 103224 RRID:AB_313007 |
| PE-Dazzle 594-conjugated anti-B220 (RA3-6B2) | Biolegend | catalog no. 103258 RRID:AB_2564053 |
| PE-Dazzle 594-conjugated anti-CXCR6 (SA051D1) | Biolegend | catalog no. 151117 RRID:AB_2721700 |
| BV605-conjugated anti-Ly-108 (13G3) | BD Biosciences | catalog no. 745250 RRID:AB_2742834 |
| BV650-conjugated anti-SLAM/CD150 (TC15-12F12.2) | Biolegend | catalog no. 115932 RRID:AB_2715765 |
| FITC-conjugated anti-CD69 (H1.2F3) | Biolegend | catalog no. 104506 RRID:AB_313109 |
| BV605-conjugated anti-CX3CR1 (SA011F11) | Biolegend | catalog no. 149027 RRID:AB_2565937 |
| PE-Cy7-conjugated anti-LAG3 (C9B7W) | Biolegend | catalog no. 125226 RRID:AB_2715764 |
| BV421-conjugated anti-Tim-3 (RMT3-23) | Biolegend | catalog no. 119723 RRID:AB_2616908 |
| APC-conjugated anti-Tim-3 (RMT3-23) | Biolegend | catalog no. 119706 RRID:AB_2561656 |
| eFluor660-conjugated anti-TOX (TXRX10) | Thermo Fisher Scientific | catalog no. 50-6502-82 RRID:AB_2574265 |
| unconjugated anti-TCF-1 | Cell Signaling Technology | catalog no. 2203 RRID:AB_2199302 |
| BV421-conjugated anti-BCL6 (K112-91) | BD Biosciences | catalog no. 563363 RRID:AB_2738159 |
| PE-conjugated anti-IFN-g (XMG1.2) | Biolegend | catalog no. 505808 RRID:AB_315402 |
| APC-conjugated anti-IL-2 (JES6-5H4, BD Pharmingen) | BD Biosciences | catalog no. 554429 RRID:AB_398555 |
| APC-conjugated TNF-a (MP6-XT22) | Biolegend | catalog no. 506308 RRID:AB_315429 |
| MojoSort Mouse CD4 T Cell Isolation Kit | Biolegend | catalog no. 480033 RRID: N/A |
| APC-Cy7-conjugated anti-CD4 | Biolegend | catalog no. 100414 RRID:AB_312699 |
| Bacterial and virus strains | ||
| LCMV-Armstrong | Prepared in Lab | N/A |
| LCMV-clone 13 | Prepared in Lab | N/A |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| RPMI-1640 | GenDEPOT | catalog no. CM059-050 |
| LCMV-gp61-80 peptide | GenScript Biotech | Custom order |
| Brefeldin A | Sigma | catalog no. B6542 |
| Foxp3 staining kit | eBioscience | catalog no. 00-5523-00 |
| Collagenase B | Sigma | catalog no. C9891 |
| Collagenase D1 | Roche | catalog no. 11088882001 |
| DNase I | Sigma | catalog no. 10104159001 |
| Percoll | Sigma | catalog no. P4937 |
| Critical commercial assays | ||
| Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell | 10× Genomics | 1000071 |
| Chromium Single Cell 5' Library Construction Kit | 10× Genomics | 1000020 |
| Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 | 10× Genomics | 1000165 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, 16 rxns | 10× Genomics | PN-1000175 |
| Deposited data | ||
| Raw and processed data | This paper | GEO: GSE181474 |
| Experimental models: Cell lines | ||
| Fibrosarcoma cell line 1956-mOVA | Laboratory of Kenneth Murphy | Ferris et al., 2020 |
| Experimental models: Organisms/strains | ||
| C57BL/6N (B6) mice | Charles River Laboratories | Strain Code 556 PPID: N/A |
| B6-CD45.1 mice | Charles River Laboratories | RRID: IMSR_CRL:564 |
| C57BL/6N (B6) mice | Jackson Laboratory | RRID: IMSR_JAX:000664 |
| B6-CD45.1 mice | Jackson Laboratory | RRID: IMSR_JAX:002014 |
| Prdm1-EYFP mice | Jackson Laboratory | RRID: IMSR_JAX:008828 |
| Bcl6-flox mice | Jackson Laboratory | RRID: IMSR_JAX:023727 |
| Cd40lg-cre mice | This paper | N/A |
| Actb-Flpe mice | Jackson Laboratory | RRID: IMSR_JAX:005703 |
| OT-II mice | Jackson Laboratory | RRID: IMSR_JAX:004194 |
| B6.129X1-Gt (ROSA)26Sortm1(EYFP)Cos/J | Jackson Laboratory | RRID: IMSR_JAX:006148 |
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and algorithms | ||
| GraphPad Prism, version 9.3.1(350) | Graph Pad | RRID:SCR_002798 |
| Flowjo 10.8.0 | Flowjo, LLC | RRID:SCR_008520 |
| Cell Ranger, version 3.1.0 | 10× Genomics | https://support.10xgenomics.com/single-cell-vdj/software |
| Cell Ranger ATAC, version 1.2.0 | 10× Genomics | https://support.10xgenomics.com/single-cell-atac/software |
| Seurat, version 3.1.1 |
Stuart et al., 2019 PMID: 31178118 |
https://satijalab.org/seurat |
| Monocle 3, version 0.2.1 |
Cao et al., 2019 PMID: 30787437 |
https://cole-trapnell-lab.github.io/monocle3/ |
| R, version 3.6.1 | The R Project | https://www.r-project.org/ |
| ArchR, version 1.0.1 | Granja et al., 2019 PMID: 33633365 |
RRID:SCR_020982 https://www.nature.com/articles/s41587-019-0332-7 |
| Other | ||
| PE- or APC-labeled I-Ab-LCMV-gp66 tetramer | NIH Tetramer Core at Emory | N/A |
| PE- or APC-labeled H2-Db-LCMV-gp33 tetramer | MBL | TB-M512-1 RRID: N/A |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | Thermo Fisher Scientific |
L34965 RRID: N/A |
| CellTrace™ CFSE Cell Proliferation Kit, for flow cytometry | Life technologies |
C34554 RRID: N/A |