KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| AF488-conjugated anti-rabbit IgG | Thermofisher | Cat#A11034; RRID: AB_2576217 |
| AF647-conjugated anti-rabbit IgG | BioLegend | Cat#406414; RRID: AB_2563202 |
| APC-Cy7-conjugated anti-B220 (Clone:RA3-6B2) | BioLegend | Cat#103224; RRID: AB_313006 |
| BV510-conjugated anti-B220 (Clone:RA3-6B2) | BioLegend | Cat# 103247; RRID: AB_2561394 |
| PerCP-Cy5.5-conjugated anti-B220 (Clone: RA3-6B2) | BioLegend | Cat#103236; RRID: AB_893354 |
| BV605-conjugated anti-B220 (Clone:RA3-6B2) | BioLegend | Cat#103243; RRID: AB_11203907 |
| PE-Dazzle-conjugated anti-B220 (Clone:RA3-6B2) | BioLegend | Cat#103258; RRID: AB_2564053 |
| APC-conjugated anti-CCR7 (Clone:4B12) | BioLegend | Cat#120108; RRID: AB_389233 |
| PE-Cy7-conjugated anti-CD11b (Clone:M1/70) | BioLegend | Cat#101216; RRID: AB_312798 |
| BV421-conjugated anti-CD127 (Clone:A7R34) | BioLegend | Cat#135024; RRID: AB_10897948 |
| AF700-conjugated anti-CD19 (Clone:6D5) | BioLegend | Cat#115528; RRID: AB_493734 |
| APC-conjugated anti-CD25 (Clone:PC61) | BioLegend | Cat#102012; RRID: AB_312860 |
| BV605-conjugated anti-CD25 (Clone:PC61) | BioLegend | Cat#102035; RRID: AB_11126977 |
| FITC-conjugated anti-CD25 (Clone:PC61) | BioLegend | Cat#102006; RRID: AB_312854 |
| PE-conjugated anti-CD25 (Clone:PC61) | BioLegend | Cat#102008; RRID: AB_312856 |
| APC-conjugated anti-CD4 (Clone:GK1.5) | BioLegend | Cat#100412; RRID: AB_312696 |
| APC-Cy7-conjugated anti-CD4 (Clone:GK1.5) | BioLegend | Cat#100414; RRID: AB_312698 |
| BUV395-conjugated anti-CD4 (Clone:GK1.5) | BD | Cat#563790; RRID: AB_2738426 |
| BV510-conjugated anti-CD4 (Clone:RM4-5) | BioLegend | Cat#100559; RRID: AB_2561388 |
| BV711-conjugated anti-CD4 (Clone:RM4-5) | BioLegend | Cat#100550; RRID: AB_2562099 |
| BV785-conjugated anti-CD4 (Clone:RM4-5) | BioLegend | Cat#100551; RRID: AB_2563053 |
| PerCP-Cy5.5-conjugated anti-CD4 (Clone:GK1.5) | BioLegend | Cat#100434; RRID: AB_893324 |
| AF700-conjugated anti-CD44 (Clone:IM7) | BioLegend | Cat#103026; RRID: AB_493712 |
| Pacific Blue-conjugated anti-CD44 (Clone:IM7) | BioLegend | Cat#103020; RRID: AB_493682 |
| AF700-conjugated anti-CD45 (Clone:30-F11) | BioLegend | Cat#103128; RRID: AB_493714 |
| BV570-conjugated anti-CD45.1 (Clone:A20) | BioLegend | Cat#110733; RRID: AB_10895765 |
| BV605-conjugated anti-CD45.1 (Clone:A20) | BioLegend | Cat#110738; RRID: AB_2562565 |
| PE-Cy7-conjugated anti-CD45.1 (Clone:A20) | BioLegend | Cat#110730; RRID: AB_1134170 |
| AF700-conjugated anti-CD45.2 (Clone:104) | BioLegend | Cat#109822; RRID: AB_493730 |
| APC-Cy7-conjugated anti-CD45.2 (Clone:104) | BioLegend | Cat#109824; RRID: AB_830788 |
| FITC-conjugated anti-CD45.2 (Clone:104) | BioLegend | Cat#109806; RRID: AB_313442 |
| APC-Fire750-conjugated anti-CD62L (Clone: MEL-14) | BioLegend | Cat#104450; RRID: AB_2629771 |
| FITC-conjugated anti-CD62L (Clone:MEL-14) | BioLegend | Cat#104406; RRID: AB_313092 |
| PE-conjugated anti-CD62L (Clone:MEL-14) | BD | Cat#553151; RRID: AB_394666 |
| PerCP-Cy5.5-conjugated anti-CD62L (Clone: MEL-14) | BioLegend | Cat#104432; RRID: AB_2187123 |
| FITC-conjugated anti-CD69 (Clone:H1.2F3) | BioLegend | Cat#104506; RRID: AB_313108 |
| APC-Cy7-conjugated anti-CD8a (Clone:53-6.7) | BioLegend | Cat#100714; RRID: AB_312752 |
| BUV395-conjugated anti-CD8a (Clone:53-6.7) | BD | Cat#565968; RRID: AB_2732919 |
| BV785-conjugated anti-CD8a (Clone:53-6.7) | BioLegend | Cat#100749; RRID: AB_11218801 |
| PE-Cy7-conjugated anti-CD8a (Clone:53-6.7) | BioLegend | Cat#100722; RRID: AB_312760 |
| BV605-conjugated anti-CD8a (Clone:53-6.7) | BioLegend | Cat#100744; RRID: AB_2562609 |
| FITC-conjugated anti-CD8a (Clone:53-6.7) | BioLegend | Cat#100706; RRID: AB_312744 |
| PerCP-Cy5.5-conjugated anti-CD8b (Clone: YTS156.7.7) | BioLegend | Cat#126610; RRID: AB_2260149 |
| BV605-conjugated anti-CX3CR1 (Clone: SA011F11) | BioLegend | Cat#149027; RRID: AB_2565937 |
| BV785-conjugated anti-CX3CR1 (Clone: SA011F11) | BioLegend | Cat#149029; RRID: AB_2565938 |
| BV711-conjugated anti-CXCR5 (Clone:L138D7) | BioLegend | Cat#145529; RRID: AB_2734207 |
| PE-Dazzle-conjugated anti-CXCR6 (Clone: SA051D1) | BioLegend | Cat#151117; RRID: AB_2721699 |
| PE-cy5-conjugated anti-Gzmb (Clone:QA16A02) | BioLegend | Cat#372226; RRID: AB_2910421 |
| AF700-conjugated anti-Ki67 (Clone:B56) | BD | Cat#561277; RRID: AB_10611571 |
| BV650-conjugated anti-Ki67 (Clone:B56) | BD | Cat#563757; RRID: AB_2688008 |
| APC-Cy7-conjugated anti-KLRG1 (Clone:2F1) | BioLegend | Cat#138426; RRID: AB_2566553 |
| FITC-conjugated anti-KLRG1 (Clone:2F1) | BioLegend | Cat#138410; RRID: AB_10643582 |
| PE-Cy7-conjugated anti-KLRG1 (Clone:2F1) | BioLegend | Cat#138416; RRID: AB_2561735 |
| PE-Cy7-conjugated anti-LAG3 (Clone:C9B7W) | Thermofisher | Cat#25-2231-82; RRID: AB_2573428 |
| BB700-conjugated anti-Ly108 (Clone:13G3) | BD | Cat#742272; RRID: AB_2871448 |
| BV605-conjugated anti-Ly108 (Clone:13G3) | BD | Cat#745250; RRID: AB_2742834 |
| BV650-conjugated anti-NK1.1 (Clone:PK136) | BioLegend | Cat#108735; RRID: AB_11147949 |
| BV750-conjugated anti-PD1 (Clone:29F.1A12) | BioLegend | Cat#135263; RRID: AB_2941421 |
| FITC-conjugated anti-PD1 (Clone:29F.1A12) | BioLegend | Cat#135214; RRID: AB_10680238 |
| PE-Cy7-conjugated anti-PD1 (Clone:29F.1A12) | BioLegend | Cat#135216; RRID: AB_10689635 |
| PE-Cy7-conjugated anti-Sca1 (Clone:E13-161.7) | BioLegend | Cat#122514; RRID: AB_756198 |
| BV650-conjugated anti-SLAM (Clone:TC15-12F12.2) | BioLegend | Cat#115931; RRID: AB_2562402 |
| PE-Cy7-conjugated anti-Tbet (Clone:4B10) | BioLegend | Cat#644823; RRID: AB_2561760 |
| Unconjugated anti-TCF1 (Clone:C63D9) | Cell Signaling | Cat#2203S; RRID: AB_2199302 |
| APC-Cy7-conjugated anti-TCR Va2 (Clone:B20.1) | BioLegend | Cat#127818; RRID: AB_10682897 |
| FITC-conjugated anti-TCR Vb8.1,8.2 (Clone: KJ16-133.18) | BioLegend | Cat#118406; RRID: AB_1227787 |
| AF700-conjugated anti-Thy1.1 (Clone:OX-7) | BioLegend | Cat#202528; RRID: AB_1626241 |
| Pacific Blue-conjugated anti-Thy1.1 (Clone:OX-7) | BioLegend | Cat#202522; RRID: AB_1595477 |
| PE-conjugated anti-Thy1.1 (Clone:OX-7) | BioLegend | Cat#202524; RRID: AB_1595524 |
| PerCP-Cy5.5-conjugated anti-Thy1.2 (Clone:53-2.1) | BioLegend | Cat#140322; RRID: AB_2562696 |
| BV421-conjugated anti-TIM3 (Clone:RMT3-23) | BioLegend | Cat#119723; RRID: AB_2616908 |
| eFluor660-conjugated anti-TOX (Clone:TXRX10) | Thermofisher | Cat#50-6502-82; RRID: AB_2574265 |
| PerCP/Fire 806 -conjugated anti-LAG3 (Clone:C9B7W ) | BioLegend | Cat#125249; RRID: AB_3068219 |
| APC-conjugated anti-TIGIT (Clone:VSIG9) | BioLegend | Cat#142106; RRID: AB_10960139 |
| Unconjugated anti-IRF4 (Clone:D9P5H) | Cell Signaling | Cat#15106S; RRID: AB_2798709 |
| PE-Dazzle-conjugated anti-CD73 (Clone: TY/11.8) | BioLegend | Cat#127233; RRID: AB_2800628 |
| anti-PD-L1(Clone: 10F.9G2) | Leinco | Cat# P363; RRID:AB_2749826 |
| anti-CD3 (Clone: 145-2C11) | BioXcell | Cat # BE0001-1; RRID: AB_1107634 |
| anti-CD28 (Clone: 37.51) | BioXcell | Cat # BE0015-1; RRID: AB_1107624 |
| anti-Hamster IgG | MP bio | Cat#0855397 |
| anti-IL-2 (Clone: S4B6) | BioXcell | Cat # BE0043-1; RRID: AB_1107705 |
| anti-IL-2(Clone: JES6-1A12) | BioLegend | Cat # 503706; RRID: AB_315291 |
|
| ||
| Bacterial and virus strains | ||
|
| ||
| LCMV-Armstrong | prepared in lab | N/A |
| LCMV-clone 13 | prepared in lab | N/A |
| Listeria monocytogenes-GP | DMX | Cat#09-080 |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Carboxyfluorescein succinimidyl ester (CFSE) | Sigma Aldrich | Cat#21888 |
| LCMV-gp33-41 peptide | GenScript | custom ordered |
| ERCC Spike-in control RNA | Thermofisher | Cat# 4456740 |
| DNaseI | Sigma Aldrich | Cat # 260913-10MU |
| Liberase | Sigma Aldrich | Cat#5401020001 |
| Cas9 V3 nuclease | IDT | Cat#1081059 |
| Diphtheria toxin | Sigma Aldrich | Cat # D0564 |
| Tamoxifen | Sigma Aldrich | Cat #T5648 |
| Recombinant mouse IL-2 | PeproTech | Cat # 212-12 |
| Recombinant mouse IL-12 | R&D | Cat # 419-ML-010 |
| Recombinant mouse IL-15 | PeproTech | Cat # 200-15 |
| Brefeldin A | Biolegend | Cat# 420601 |
| 4% paraformaldehyde | Electron Microscopy | Cat# 15710 |
| DNase | Worthington | Cat # LS002007 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Alt-R Cas9 Electroporation Enhancer | IDT | Cat#1075915 |
| P3 Primary Cell 4D-Nucleofector® X Kit S | Lonza | Cat# V4XP-3032 |
| Precision Count Beads | BioLegend | Cat # 424902 |
| Dynabeads FlowComp Mouse CD8 isolation kit | Thermofisher | Cat #114-62D |
| MojoSort CD8 T cell negative enrichment kit | Biolegend | Cat # 480035 |
| Lymphopure lymphocyte separation medium | Biolegend | Cat # 426202 |
| LIVE/DEAD Aqua | Thermofisher | Cat # L34966 |
| LIVE/DEAD Near-IR | Thermofisher | Cat # L34976 |
| eBioscience Foxp3 / Transcription Factor Staining Buffer kit | Thermofisher | Cat # 50-112-8857 |
| TriReagent | Sigma | Cat # T9424-200ML |
| qScript cDNA SuperMix | Quantabio | Cat # 95048-500 |
| Luminaris Color HiGreen qPCR Master Mix | Thermofisher | Cat # K0394 |
| Protease inhibitor cocktail | Sigma Aldrich | Cat# P8340 |
| QIAquick PCR Purification Kit | Qiagen | Cat# 28104 |
| Direct-zol RNA Microprep Kit | Zymo Research | Cat# R2062 |
| Tagment DNA TDE1 Enzyme and Buffer Small Kit | Illumina | Cat # 20034197 |
| AMPure XP beads | Beckman Coulter | Cat # A63880 |
| EZ DNA Methylation-Direct Kit | Zymo Research | Cat # D5021 |
| Zymoclean Gel DNA Recovery Kit | Zymo Research | Cat # D4008 |
| Native Barcoding Kit 24 V14 | Oxford Nanopore Technologies | Cat# SQK-NBD114.24 |
| 10x Genomics Single Cell Immune Profiling Solution Kit | N/A | |
|
| ||
| Deposited data | ||
|
| ||
| scATAC-seq of 8 dpi LCMVArm | this paper | GEO: GSE295247 |
| scRNA-seq of 8 dpi LCMVArm | this paper | GEO: GSE295246 |
| Bulk ATAC-seq of TPEX and TEX | this paper | GEO: GSE294878 |
| Bulk ATACseq of WT, Prdm1, Tcf7, and DKO TPEX | this paper | GEO: GSE294879 |
| Bulk RNA-seq of Prdm1 fate mapped effector T cells | this paper | GEO: GSE294880 |
| Bulk RNA-seq of WT, Prdm1, Tcf7, and DKO TPEX | this paper | GEO: GSE294881 |
| Bulk RNA-seq of WT and Tcf7Δ+17kb/+22kb effector T cells | this paper | GEO: GSE294882 |
| Bulk ATAC-seq of naive, SLEC, and Tcm cells | Scott-Browne et al.48 | GEO: GSE88987 |
| ChIP-seq of AP4 in CD8+ T cells | Chou et al.25 | GEO: GSE58075 |
| ChIP-seq of BATF and IRF4 in CD4+ T cells | Iwata et al.49 | GEO: GSE85172 |
| Raw data corresponding to main figures | this paper | Mendeley Data: https://doi.org/10.17632/6xjrfdh9pz.1 |
| Raw data corresponding to supplemental figures | this paper | Mendeley Data: https://doi.org/10.17632/yrn6xk4227.1 |
| ChIP-seq of Blimp1 in CD8+ T cells | Mackay et al.20 | GEO: GSE79339 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| MC38.gpLaboratory of Arlene Sharpe | Laboratory of Arlene Sharpe | N/A |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Mouse: Tcf7Δ+22kb | This paper | N/A |
| Mouse: Tcf7ΔAICE−22 | This paper | N/A |
| Mouse: Tcf7ΔEbox−22 | This paper | N/A |
| Mouse: Tcf7ΔBlimp1−22 | This paper | N/A |
| Mouse: Prdm1creERT2 | This paper | N/A |
| Mouse: C57BL/6-cBrd/cBrd/Cr (C57BL/6 albino) | Charles River | Strain #:562 |
| Mouse: Actb-Flpe | Jackson Laboratory | Strain #:005703; RRID:IMSR_JAX:005703 |
| Mouse: C57BL/6NJ | Jackson Laboratory | Strain #:005304; RRID:IMSR_JAX:005304 |
| Mouse: Prdm1YFP | Jackson Laboratory | Strain #:008828; RRID:IMSR_JAX:008828 |
| Mouse: Batf−/− | Jackson Laboratory | Strain #:013758; RRID:IMSR_JAX:013758 |
| Mouse: Prdm1F/F | Jackson Laboratory | Strain #:008100; RRID:IMSR_JAX:008100 |
| Mouse: Tcf7GFP | Jackson Laboratory | Strain #:030909; RRID:IMSR_JAX:030909 |
| Mouse: Rosa26LSL-tdTomato (Ai9) | Jackson Laboratory | RRID:IMSR_JAX:007909 |
| Mouse: Irf4−/− | Laboratory of Kenneth Murphy | Strain #:031834; RRID:IMSR_JAX:031834 |
| Mouse: P14-TCR transgenic | Jackson Laboratory | MMRRC Strain #037394-JAX; RRID: MMRRC_037394-JAX |
| Mouse: Tcf7GFP-DTR | Siddiqui et al.50 | N/A |
| Mouse: Cd8 (E8I)-cre mice | Jackson Laboratory | Strain #:008766; RRID:IMSR_JAX:008766 |
| Mouse: Tfap4F/F | Chou et al., 2015 | N/A |
| Mouse: B6-CD45.1 congenic | Charles River Laboratories | RRID: IMSR_CRL:564 |
| Mouse: B6-CD45.1 isogenic | Jackson Laboratory | Strain #:033076; RRID:IMSR_JAX:033076 |
|
| ||
| Oligonucleotides | ||
|
| ||
| See Table S1 for oligonucleotide sequences | N/A | |
|
| ||
| Software and algorithms | ||
|
| ||
| Cell Ranger | 10x Genomics | |
| Seurat R Package | Stuart et al.51 PMID: 31178118 | https://satijalab.org/seurat |
| ArchR (version 1.0.2) | Granja et al.35; PMID: 33633365 | RRID: SCR_020982 https://www.nature.com/articles/s41587-019-0332-7 |
| Prism 10 | GraphPad | https://www.graphpad.com/; RRID:SCR_002798 |
| FlowJo (version 10.9.0) | Treestar | https://www.flowjo.com/; RRID:SCR_008520 |
|
| ||
| Other | ||
|
| ||
| AF488-conjugated anti-H-2Db FQPQNGQFI | NIH Tetramer core | N/A |
| PE-conjugated anti-H2-Db KAVYNFATC | NIH Tetramer core | N/A |
| APC-conjugated anti-H2-Db KAVYNFATC | NIH Tetramer core | N/A |