Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (M. musculus) | C57BL/6J background | Jackson Laboratory | Stock No. 000664 RRID:IMSR_JAX:000664 |
|
| Genetic reagent (M. musculus) | B6.C-H2d/bByJ | Jackson Laboratory | Stock No. 000359 RRID:IMSR_JAX:000359 |
|
| Genetic reagent (M. musculus) | B6(Cg)-Rag2tm1.1Cgn/J | Jackson Laboratory | Stock No. 008449 RRID:IMSR_JAX:008449 |
|
| Genetic reagent (M. musculus) | B6.129S7-Rag1tm1Mom | Jackson Laboratory | Stock No. 002216 RRID:IMSR_JAX:002216 |
|
| Genetic reagent (M. musculus) | B6.129P2-b2mtm1Unc/DcrJ | Jackson Laboratory | Stock No. 002087 RRID:IMSR_JAX:002087 |
|
| Genetic reagent (M. musculus) | B6.129S6-Rag2tm1Fwa Tg(TcraTcrb)1100Mjb | Taconic | Model No. 2334 RRID:IMSR_TAC:2334 |
|
| Genetic reagent (M. musculus) | F5 Rag1−/− | Au-Yeung et al., 2014 | Generated by crossing in Au-Yeung et al., 2014, and maintained in house | |
| Genetic reagent (M. musculus) | B6xB6C (H2b/d) | Chu et al., 2016 | Generated by crossing in Chu et al., 2016, and maintained in house | |
| Genetic reagent (M. musculus) | TG6 H2b | Chu et al., 2016 | Generated by crossing in Chu et al., 2016, and maintained in house | |
| Genetic reagent (M. musculus) | TG6 H2b/d | This paper and Tsitsiklis et al., 2020 | Generated by crossing TG6tg mice from Chu et al., 2016 with B6.C-H2d/bByJ mice from Jackson Labs | |
| Genetic reagent (M. musculus) | TG6 H2b/dRag2−/− | This paper | Generated by crossing TG6tg H2b/d mice with B6(Cg)-Rag2tm1.1Cgn/J mice from Jackson Labs | |
| Genetic reagent (M. musculus) | TG6 H2bRag2−/− | This paper | Generated by crossing TG6tg H2b mice with B6(Cg)-Rag2tm1.1Cgn/J mice from Jackson Labs | |
| Genetic reagent (M. musculus) | OT-1 Rag2−/−B2M−/− | Ross et al., 2014 | Generated by crossing in Ross et al., 2014, and maintained in house | |
| Antibody | Rat Monoclonal anti-Mouse CXCR4 (Clone L276F12) PerCP-Cy5.5 | Biolegend | Cat. No. 146510 RRID:AB_2562786 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CXCR4 (Clone L276F12) APC | Biolegend | Cat. No. 146508 RRID:AB_2562784 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CCR7 (Clone 4B12) PE-Cy7 | Biolegend | Cat. No. 120124 RRID:AB_2616688 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CCR7 (Clone 4B12) PE | Biolegend | Cat. No. 120106 RRID:AB_389358 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone GK1.5) APC | Tonbo Biosciences | Cat. No. 20–0041 U100 RRID:AB_2621736 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone GK1.5) APC-Cy7 | Biolegend | Cat. No. 100414 RRID:AB_312699 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone GK1.5) Pacific Blue | Biolegend | Cat. No. 100428 RRID:AB_493647 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone RM4-5) PerCP-Cy5.5 | Tonbo Biosciences | Cat. No. 65–0042 U100 RRID:AB_2621876 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone RM4-5) PE-Cy7 | Tonbo Biosciences | Cat. No. 60–0042 U100 RRID:AB_2621829 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD4 (Clone RM4-5) BV605 | Biolegend | Cat. No. 100548 RRID:AB_2563054 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD8α (Clone 53–6.7) FITC | Biolegend | Cat. No. 100706 RRID:AB_312745 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD8α (Clone 53–6.7) PE-Cy7 | Tonbo Biosciences | Cat. No. 60–0081 U100 RRID:AB_2621832 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD8α (Clone 53–6.7) APC | Tonbo Biosciences | Cat. No. 20–0081 U100 RRID:AB_2621550 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD8α (Clone 53–6.7) BV421 | Biolegend | Cat. No. 100738 RRID:AB_11204079 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD8α (Clone 53–6.7) BV605 | Biolegend | Cat. No. 100744 RRID:AB_2562609 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD5 (Clone 53–7.3) FITC | Biolegend | Cat. No. 100606 RRID:AB_312735 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD5 (Clone 53–7.3) PE | eBioscience | Cat. No. 12-0051-83 RRID:AB_465524 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD5 (Clone 53–7.3) PE-Cy7 | Biolegend | Cat. No. 100622 RRID:AB_2562773 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD5 (Clone 53–7.3) BV421 | BD Biosciences | Cat. No. 562739 RRID:AB_2737758 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-Mouse CD69 (Clone H1.2F3) FITC | Invitrogen | Cat. No. 11-0691-85 RRID:AB_465120 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-Mouse CD69 (Clone H1.2F3) PerCP-Cy5.5 | Biolegend | Cat. No. 104522 RRID:AB_2260065 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-Mouse CD69 (Clone H1.2F3) PE-Cy7 | eBioscience | Cat. No. 25-0691-82 RRID:AB_469637 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-Mouse CD69 (Clone H1.2F3) Pacific Blue | Biolegend | Cat. No. 104524 RRID:AB_2074979 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse CD24 (Clone M1/69) Pacific Blue | Biolegend | Cat. No. 101820 RRID:AB_572011 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-Mouse TCR beta (Clone H57-597) PerCP-Cy5.5 | eBioscience | Cat. No. 45-5961-82 RRID:AB_925763 |
(1:200) |
| Antibody | Armenian Hamster Monoclonal anti-mouse TCR beta (Clone H57-597) AF647 | Biolegend | Cat. No. 109218 RRID:AB_493346 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse Valpha2 (Clone B20.1) APC | Biolegend | Cat. No. 127810 RRID:AB_1089250 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse Vbeta8.1/8.2 (Clone KJ16-133.18) FITC | Biolegend | Cat. No. 118406 RRID:AB_1227786 |
(1:200) |
| Antibody | Rat Monoclonal anti-Mouse Vbeta2 (Clone B20.6) PE | Biolegend | Cat. No. 127908 RRID:AB_1227784 |
(1:200) |
| Antibody | Mouse Monoclonal anti-Mouse Nur77 (Clone 12.14) | ThermoFisher Scientific | Cat. No. 12-5965-82 RRID:AB_1257209 |
(1:100) |
| Chemical Compound, drug | 5-ethynyl-2′-deoxyuridine (EdU) | ThermoFisher Scientific | Cat. No. A10044 | |
| Chemical Compound, drug | GTG-NuSieve Agarose | Lonza | Cat. No.: 50081 | 4% in HBSS for Thymic Slicing |
| Commercial Assay or Kit | Transcription Factor Staining Buffer Set (Invitrogen) | ThermoFisher Scientific | Cat. No. 00-5523-00 | |
| Commercial Assay or Kit | Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit (Invitrogen) | ThermoFisher Scientific | Cat. No. C10420 | |
| Commercial Assay or Kit | Quick-RNA Microprep Kit | Zymo Research | Cat. No. R1050 | |
| Software, algorithm | GraphPad PRISM | GraphPad Software | RRID:SCR_002798 | |
| Software, algorithm | Fiji/Image J software | Fiji-Image J |
https://imagej.nih.gov/ij/
RRID:SCR_003070 |
|
| Software, algorithm | FlowJo | FlowJo |
https://www.flowjo.com/
RRID:SCR_008520 |
|
| Software, algorithm | Zen | Zeiss | RRID:SCR_013672 | |
| Software, algorithm | Imaris | Bitplane Scientific | RRID:SCR_007370 | |
| Software, algorithm | DISCit | Moreau et al., 2012 | ||
| Software, algorithm | R Project for Statistical Computing | R Project for Statistical Computing | RRID:SCR_001905 | |
| Software, algorithm | Trimmomatic | Bolger et al., 2014 | ||
| Software, algorithm | Bowtie 2 | Langmead and Salzberg, 2012 | ||
| Software, algorithm | RSEM | Li and Dewey, 2011 | ||
| Software, algorithm | DESeq2 | Love et al., 2014 | ||
| Software, algorithm | FGSEA | Korotkevich and Sukhov, 2019 | ||
| Software, algorithm | MSigDB | Liberzon et al., 2011 | ||
| Software, algorithm | GEOquery | Davis and Meltzer, 2007 | ||
| Software, algorithm | Limma | Ritchie et al., 2015 | ||
| Software, algorithm | Ilustrator CS5 | Adobe | RRID:SCR_010279 | |
| Other | 0.4 mm transwell inserts | Corning | Cat. No. 353090 | |
| Other | Ghost Dye Violet 510 Live/Dead dye | Tonbo Biosciences | Cat. No. 13–0870 T100 | 1:1000 flow cytometry |
| Other | Cell Proliferation Dye eFluor450 | ThermoFisher Scientific | Cat. No. 65-0863-18 | 0.5 μM at 107 cells/ml at 37°C for 15 min in PBS |
| Other | Cell Proliferation Dye eFluor670 | ThermoFisher Scientific | Cat. No. 65-0840-85 | 0.5 μM 107 cells/ml at 37°C for 15 min in PBS |
| Other | Indo-1LR | ThermoFisher Scientific | Cat. No. I1226 | 2 mM at 3× 106 cells/ml in complete RPMI for 90 min at 37°C. Followed by 60 min recovery in RPMI at 37°C |