Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-B220-Biotin (Clone RA3-6B2) | BD | Cat#553086; RRID: AB_ 394615 |
| Anti-CD3e-FITC (Clone 145-2C11) | BD | Cat#553062; RRID: AB_394595 |
| Anti-CD3e-Biotin (Clone 145-2C11) | eBioscience | Cat#13-0031-85; RRID: AB_466319 |
| Anti-CD4-BUV395 (Clone GK1.5) | BD | Cat#563790; RRID: AB_2738426 |
| Anti-CD4-Biotin (Clone GK1.5) | eBioscience | Cat#13-0041-85; RRID: AB_466326 |
| Anti-CD4-BUV737 (Clone GK1.5) | BD | Cat#564298 |
| Anti-CD5-Biotin (Clone 53-7.3) | BD | Cat#553019; RRID: AB_394557 |
| Anti-CD8-Biotin (Clone 53-6.7) | eBioscience | Cat#13-0081-85; RRID: AB_466347 |
| Anti-CD11b-FITC (Clone M1/70) | BD | Cat#553310; RRID: AB_396679 |
| Anti-CD11b-PerCP-Cy™5.5 (Clone M1/70) | BD | Cat#550993; RRID: AB_394002 |
| Anti-CD11b-BUV737 (Clone M1/70) | BD | Cat#612800; RRID: AB_2738811 |
| Anti-CD11b-Biotin (Clone M1/70) | BD | Cat#553309; RRID: AB_394773 |
| Anti-CD14-Biotin (Clone Sa2-8) | eBioscience | Cat#13-0141-85; RRID: AB_466371 |
| Anti-CD19-PE (Clone 1D3) | BD | Cat#553786; RRID: AB_395050 |
| Anti-CD19-Biotin (Clone 1D3) | eBioscience | Cat#13-0193-85; RRID: AB_657658 |
| Anti-CD25-FITC (Clone 7D4) | BD | Cat#553072; RRID: AB_394603 |
| Anti-CD27-BV605 (Clone LG.3A10) | BD | Cat#563365; RRID: AB_2738160 |
| Anti-CD44-eFluor 450 (Clone IM7) | eBioscience | Cat#48-0441-82; RRID: AB_1272246 |
| Anti-CD44-APC-eFluor 780 (Clone IM7) | eBioscience | Cat#47-0441-82; RRID: AB_1272244 |
| Anti-CD45.1-PE-Cy™7 (Clone A20) | BD | Cat#560578; RRID: AB_1727488 |
| Anti-CD45.2-BUV395 (Clone 104) | BD | Cat#564616; RRID: AB_2738867 |
| Anti-CD45.2-BUV737 (Clone 104) | BD | Cat#612778; RRID: AB_2870107 |
| Anti-CD49a-BV421 (Clone Ha31/8) | BD | Cat#740046; RRID: AB_2739815 |
| Anti-CD49a-BV711 (Clone Ha31/8) | BD | Cat#564863; RRID: AB_2738987 |
| Anti-CD49b-APC (Clone DX5) | BD | Cat#560628; RRID: AB_1727502 |
| Anti-CD49b-eFluor 780 (Clone DX5) | eBioscience | Cat#47-5971-82; RRID: AB_11218895 |
| Anti-CD62L-PE (Clone MEL-14) | eBioscience | Cat#12-0621-82; RRID: AB_465721 |
| Anti-CD62L-APC (Clone MEL-14) | eBioscience | Cat#17-0621-82; RRID: AB_469410 |
| Anti-CD117-APC-H7 (Clone 2B8) | BD | Cat#560185; RRID: AB_1645231 |
| Anti-CD117-PE (Clone 2B8) | BD | Cat#553355; RRID: AB_394806 |
| Anti-CD122-BV786 (Clone TM-β1) | BD | Cat#740869; RRID: AB_2740521 |
| Anti-CD122-FITC (Clone 5H4) | BD | Cat#554452; RRID: AB_395401 |
| Anti-CD127-PE-Cyanine7 (Clone A7R34) | eBioscience | Cat#25-1271-82; RRID: AB_469649 |
| Anti-CD244.2-BUV395 (Clone 2B4) | BD | Cat#740226; RRID: AB_2739974 |
| Anti-CD244.2-PE-Cyanine7 (eBio244F4) | eBioscience | Cat#25-2441-82; RRID: AB_2573432 |
| Anti-CCR6-BV421 (Clone 140706) | BD | Cat#564736; RRID: AB_2738926 |
| Anti-F4/80-Biotin (Clone BM8) | eBioscience | Cat#13-4801-85; RRID: AB_466658 |
| Anti-FceR1 alpha-Biotin (Clone MAR-1) | eBioscience | Cat#13-5898-82; RRID: AB_466783 |
| Anti-IFN-γ-Alexa Fluor® 700 (Clone XMG1.2) | BD | Cat#557998; RRID: AB_396979 |
| Anti-IFN-γ-PE-Cy™7 (Clone XMG1.2) | BD | Cat#557649; RRID: AB_396766 |
| Anti-IFN-γ-FITC (Clone XMG1.2) | BD | Cat#554411; RRID: AB_395375 |
| Anti-IL-4-Brilliant Violet 421™ (Clone 11B11) | BioLegend | Cat#504120; RRID: AB_2562102 |
| Anti-IL-4-Brilliant Violet 605™ (Clone 11B11) | BioLegend | Cat#504126; RRID: AB_2686971 |
| Anti-IL-18Rα-eFluor 450 (Clone P3TUNYA) | eBioscience | Cat#48-5183-82; RRID: AB_2574069 |
| Anti-IL-21R-PE (Clone 4A9) | BioLegend | Cat#131906; RRID: AB_1279430 |
| Anti-KLRG1-APC-eFluor 780 (Clone 2F1) | eBioscience | Cat#47-5893-82; RRID: AB_2573988 |
| Anti-Ly-6G/Ly-6C-Biotin (Clone RB6-8C5) | eBioscience | Cat#13-5931-85; RRID: AB_466801 |
| Anti-NK1.1-PE-Cy™7 (Clone PK136) | BD | Cat#552878; RRID: AB_394507 |
| Anti-NK1.1-BV650 (Clone PK136) | BD | Cat#564143; RRID: AB_2738617 |
| Anti-NKG2D-PE-CF594 (Clone CX5) | BD | Cat#562614; RRID: AB_2737677 |
| Anti-NKp46-PE (Clone 29A1.4) | BD | Cat#560757; RRID: AB_1727466 |
| Anti-TER-119-Biotin (Clone TER-119) | eBioscience | Cat#13-5921-85; RRID: AB_466798 |
| Anti-CBFβ Rabbit mAb (Clone D4N2N) | CST | Cat#62184 |
| Anti-Stat4 Rabbit mAb (Clone C46B10) | CST | Cat#2653 |
| Anti-T-bet-Alexa Fluor® 647 (Clone O4-46) | BD | Cat#561267; RRID: AB_10564093 |
| Anti-EOMES-eFluor 450 (Clone Dan11mag) | eBioscience | Cat#48-4875-82; RRID: AB_2574062 |
| Anti-Ki-67-BV786 (Clone B56) | BD | Cat#563756; RRID: AB_2732007 |
| Anti-RUNX3-PE (Clone R3-5G4) | BD | Cat#564814; RRID: AB_2738969 |
| Anti-NGFR-PE (Clone C40-1457) | BD | Cat#557196; RRID: AB_396599 |
| Anti-CD3e (Clone 2C11) | Harlan | Lot#A2022931 |
| Anti-CD28 (Clone 37.51) | Harlan | Lot#A2022929 |
| Anti-IL-4 (Clone 11B.11) | NCI-Frederick | Lot#L0412006 |
| Anti-IFN-γ (Clone XMG1.2) | Harlan | Lot#A2022930 |
| Anti-CD16/CD32 (Clone 2.4G2) | Harlan | Lot#A2083015 |
| Anti-Biotin MicroBeads | Miltenyi Biotec | Cat#130-090-485 |
| Anti-CD3/CD28 Dynabeads | Gibco | Cat#11453D |
| Alexa Fluor® 647 Mouse IgG1 κ | BD | Cat#557732; RRID: AB_396840 |
| Rat IgG2a Isotype-eFluor 450 (eBR2a) | eBioscience | Cat#48-4321-82; RRID: AB_1271999 |
| Anti-mouse IgG coated magnetic beads | Diagenode | Cat#C03010022 |
| InVivoMAb anti-mouse IL-12 p40 | BioXCell | Cat#BE0051; RRID: AB_1107698 |
| InVivoMAb rat IgG2a isotype control, anti-trinitrophenol | BioXCell | Cat#BE0089; RRID: AB_1107769 |
| Bacterial and virus strains | ||
| Toxoplasma gondii ME49 | Kawabe et al., 2017 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| IL-1β | R&D systems | Cat#401-ML |
| IL-2 | R&D systems | Cat#402-ML |
| IL-6 | PeproTech | Cat#216-16 |
| IL-7 | R&D systems | Cat#407-ML |
| IL-12 | PeproTech | Cat#210-12 |
| IL-15 | R&D systems | Cat#447-ML |
| IL-18 | R&D systems | Cat#9139-IL |
| IL-21 | R&D systems | Cat#594-ML |
| CXCL12 | R&D systems | Cat#460-SD |
| Flt-3 Ligand | R&D systems | Cat#427-FL |
| IFN-γ | PeproTech | Cat#315-05 |
| SCF | R&D systems | Cat#455-MC |
| TGF-beta 1 | R&D systems | Cat#7666-MB |
| Fixable Viability Dye eFluor™ 506 | eBioscience | Cat#65-0866-14 |
| Fixable Viability Dye eFluor™ 780 | eBioscience | Cat#65-0865-14 |
| Streptavidin-BV605 | BD | Cat#563260; RRID: AB_2869476 |
| Streptavidin-APC-R700 | BD | Cat#565144; RRID: AB_2869657 |
| Protein A-coated magnetic beads | Diagenode | Cat#C03010020 |
| Percoll Plus | GE Healthcare | Cat#17544501 |
| Polybrene | Sigma | Cat#TR-1003-G |
| ACK Lysing Buffer | Gibco | Cat#A1049201 |
| AS15-Tetramer-BV421 | NIH TCF | Order#42412 |
| AS15-Tetramer-APC | NIH TCF | Order#42413 |
| Monensin Solution | eBioscience | Cat#00-4505-51 |
| L-Glutamine | Gibco | Cat#25030 |
| Sodium pyruvate | Gibco | Cat#11360 |
| β-mercaptoethanol | Gibco | Cat#21985 |
| NEAA | Gibco | Cat#11140 |
| Penicillin and streptomycin | Gibco | Cat#15140 |
| RPMI medium 1640 | Gibco | Cat#21870-076 |
| MEM | Gibco | Cat#11095080 |
| FspI | NEB | Cat#R0135L |
| PMA (Phorbol 12-myristate 13-acetate) | Sigma | Cat#P8139 |
| Ionomycin | Sigma | Cat#407952 |
| InSolution NF-κB Activation Inhibitor | Sigma | Cat#481407-1MG |
| Polyinosinic–polycytidylic acid sodium salt | Sigma | Cat#P0913-50MG |
| EasySep™ Buffer | Stem cell | Cat#20144 |
| Cycloheximide | Sigma | Cat#C1988-1G |
| DMSO | Sigma | Cat#D2650 |
| Critical commercial assays | ||
| Foxp3 Staining Buffer Set | eBioscience | Cat#00-5523-00 |
| QuantiTect Rev. Transcription Kit | Qiagen | Cat#205313 |
| MinElute Reaction Cleanup Kit | Qiagen | Cat#28206 |
| QIAquick Gel Extraction Kit | Qiagen | Cat#28704 |
| RNeasy Plus Mini Kit | Qiagen | Cat#74136 |
| PrimeScript™ RT Master Mix | TAKARA | Cat#RR036A |
| FastStart Universal SYBR Green Master (Rox) | Roche | Cat#04913850001 |
| P4 Primary Cell 4D-Nucleofector | LONZA | Cat#V4XP-4024 |
| CD4+ T Cell Isolation Kit | Miltenyi Biotec | Cat#130-104-454 |
| EasySep™ Mouse Streptavidin RapidSpheres™ Isolation Kit | Stem cell | Cat#19860 |
| RNase-Free DNase Set | Qiagen | Cat#79256 |
| DNeasy Blood & Tissue Kit | Qiagen | Cat#69506 |
| IFN gamma Mouse Uncoated ELISA Kit | Invitrogen | Cat#88-7314-86 |
| Deposited data | ||
| ChIP-Seq and DNase-Seq data | This manuscript | GEO: GSE172358 |
| ChIP-Seq (T-bet in Th1-2) | Zhu et al., 2012 | GEO: GSE38808 |
| Experimental models: Cell lines | ||
| OP9 | Schmitt and Zúñiga-Pflücker, 2002 | N/A |
| OP9-DLL1 | Schmitt and Zúñiga-Pflücker, 2002 | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: Tbx215M/5M | This manuscript | N/A |
| Mouse: Tbx21ΔC-3 | This manuscript | N/A |
| Mouse: Tbx21ΔC-8.5 | This manuscript | N/A |
| Mouse: Tbx21ΔC-3ΔC-8.5 | This manuscript | N/A |
| Mouse: Tcra−/− | NIAID-Taconic | Taconic line 98 |
| Mouse: CD45.1 congenic | NIAID-Taconic | Taconic line 7 |
| Mouse: Rag1−/− | NIAID-Taconic | Taconic line 146 |
| Mouse: Rag2−/−γc−/− | NIAID-Taconic | Taconic line 111 |
| Mouse: T-bet-ZsGreen | NIAID-Taconic | Taconic line 8419 |
| Mouse: T-bet-ZsGreen-Tbx21−/− | NIAID-Taconic | Taconic line 8451 |
| Mouse: T-bet-ZsGreen-Stat4−/−Ifngr1−/− | NIAID-Taconic | Taconic line 8450 |
| Mouse: Il18r1−/− | The Jackson Laboratory | Stock#004131 |
| Mouse: C57BL/6J | The Jackson Laboratory | Stock#000664 |
| Mouse: RUNX3-YFP | Egawa and Littman, 2008 | Now also available at Jackson Laboratory, Stock#008774 |
| Oligonucleotides | ||
| See Excel file Table S3 | ||
| Recombinant DNA | ||
| NGFR-RUNX3 retrovirus | Yagi et al., 2010 | N/A |
| GFP-T-bet retrovirus | Yagi et al., 2010 | N/A |
| Software and algorithms | ||
| FlowJo V10 | FlowJo LLC | https://www.flowjo.com |
| Prism 7 | Graphpad | https://www.graphpad.com |
| MEME Suite | N/A | https://meme-suite.org |
| WashU Epigenome Browser | Washington University in St. Louis | http://epigenomegateway.wustl.edu |