KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse CD3 AF488 (Clone 17A2) | BioLegend | Cat#100210; RRID: AB_389301 |
| anti-mouse CD3 AF647 (Clone 145-2C11) | BioLegend | Cat#100324; RRID: AB_492861 |
| anti-mouse CD4 Biotin (Clone GK1.5) | BioLegend | Cat#100404; RRID: AB_312689 |
| anti-mouse CD4 AF647 (Clone GK1.5) | BioLegend | Cat#100424; RRID: AB_389324 |
| anti-mouse CD4 AF647 (Clone RM4-5) | BioLegend | Cat#100533; RRID: AB_493372 |
| anti-mouse CD4 BV421 (Clone GK1.5) | BioLegend | Cat#100443; RRID: AB_2562557 |
| anti-mouse CD4 BV510 (Clone RM4-5) | BD Biosciences | Cat#563106; RRID: AB_2687550 |
| anti-mouse CD8 BV421 (Clone 53-6.7) | BD Biosciences | Cat#563898; RRID: AB_2738474 |
| anti-mouse CD11b PE-Cy7 (Clone M1/70) | BioLegend | Cat#101215; RRID: AB_312798 |
| anti-mouse CD11c Biotin (Clone N418) | BioLegend | Cat#117304; RRID: AB_313773 |
| anti-mouse CD11c AF647 (Clone N418) | BioLegend | Cat#117312; RRID: AB_389328 |
| anti-mouse CD19 APC-R700 (Clone 1D3) | BD Biosciences | Cat#565473; RRID: AB_2739253 |
| anti-mouse CD21/35 AF594 (Clone 7E9) | BioLegend | Cat#123426; RRID: AB_2632698 |
| anti-mouse CD21/35 AF647 (Clone 7E9) | BioLegend | Cat#123424; RRID: AB_2629578 |
| anti-mouse CD25 BV421 (Clone PC61) | BioLegend | Cat#102043; RRID: AB_2562611 |
| anti-mouse CD43 Biotin (Clone S7) | BD Biosciences | Cat#553269; RRID: AB_2255226 |
| anti-mouse/human CD44 FITC (Clone IM7) | BioLegend | Cat#103006; RRID: AB_312957 |
| anti-mouse/human CD44 PerCP-Cy5.5 (Clone IM7) | BioLegend | Cat#103006; RRID: AB_2076204 |
| anti-mouse/human CD44 PE-594 (Clone IM7) | BioLegend | Cat#103056; RRID: AB_2564044 |
| anti-mouse CD45.1 BV421 (Clone A20) | BioLegend | Cat#110732; RRID: AB_2562563 |
| anti-mouse CD45.2 FITC (Clone 104) | Thermo Fisher Scientific | Cat#11-0454-82; RRID: AB_465061 |
| anti-mouse CD62L PerCP-Cy5.5 (Clone MEL-14) | BioLegend | Cat#104430; RRID: AB_2187124 |
| anti-mouse CD62L PE (Clone MEL-14) | BioLegend | Cat#104408; RRID: AB_313095 |
| anti-mouse CD62L BV786 (Clone MEL-14) | BD Biosciences | Cat#564109; RRID: AB_2738598 |
| anti-mouse CD69 PE-Cy5 (Clone H1.2F3) | BioLegend | Cat#104510; RRID: AB_313113 |
| anti-mouse CD90.2 Biotin (Clone 30H12) | BioLegend | Cat#105304; RRID: AB_313175 |
| anti-mouse CD90.2 AF488 (Clone 30H12) | BioLegend | Cat#105316; RRID: AB_492886 |
| anti-mouse CD90.2 PE (Clone 30H12) | BioLegend | Cat#105307; RRID: AB_313178 |
| anti-mouse CD90.2 AF647 (Clone 30H12) | BioLegend | Cat#105318; RRID: AB_492888 |
| anti-mouse CD90.2 AF700 (Clone 30H12) | BioLegend | Cat#105320; RRID: AB_493725 |
| anti-mouse CD90.2 AF700 (Clone 53-2.1) | BioLegend | Cat#140324; RRID: AB_2566740 |
| anti-mouse CD90.2 BV421 (Clone 53-2.1) | BioLegend | Cat#140327; RRID: AB_2686992 |
| anti-mouse CD138 BV308 (Clone 281-2) | BD Biosciences | Cat#563147; RRID: AB_2721029 |
| anti-mouse CD185 (CXCR5) Biotin (Clone L138D7) | BioLegend | Cat#145510; RRID: AB_2562126 |
| anti-mouse CD185 (CXCR5) Biotin (Clone 2G8) | BD Biosciences | Cat#551960; RRID: AB_394301 |
| anti-mouse CD279 (PD-1) PE-Cy7 (Clone 29F.1A12) | BioLegend | Cat#135216; RRID: AB_10689635 |
| anti-mouse CD279 (PD-1) BV421 (Clone 29F.1A12) | BioLegend | Cat#135221; RRID: AB_2562568 |
| anti-mouse/human B220 APC/Fire750 (Clone RA3-6B2) | BioLegend | Cat#103259; RRID: AB_2572108 |
| anti-mouse/human B220 BV605 (Clone RA3-6B2) | BioLegend | Cat#103244; RRID: AB_2563312 |
| anti-mouse/human B220 BV785 (Clone RA3-6B2) | BioLegend | Cat#103246; RRID: AB_2563256 |
| anti-mouse/human Bcl-6 PE (Clone K112-91) | BD Biosciences | Cat#561522; RRID: AB_10717126 |
| anti-mouse/human Bcl-6 PE-CF594 (Clone K112-91) | BD Biosciences | Cat#562401; RRID: AB_11152084 |
| anti-mouse/human Bcl-6 AF647 (Clone K112-91) | BD Biosciences | Cat#561525; RRID: AB_10898007 |
| anti-mouse DO11.10 TCR FITC (Clone KJ1-26) | Thermo Fisher Scientific | Cat#11-5808-82; RRID: AB_465248 |
| anti-mouse F4/80 Biotin (Clone BM8) | BioLegend | Cat#123106; RRID: AB_893501 |
| anti-mouse F4/80 PE (Clone BM8) | BioLegend | Cat#123110; RRID: AB_893486 |
| anti-mouse FoxP3 AF488 (Clone FJK-16s) | Thermo Fisher Scientific | Cat#53-5773-82; RRID: AB_763537 |
| anti-mouse FoxP3 AF647 (Clone MF23) | BD Biosciences | Cat#560401; RRID: AB_1645201 |
| anti-GFP AF488 (Clone FM264G) | BioLegend | Cat#338008; RRID: AB_2563288 |
| anti-mouse GL7 FITC (Clone GL7) | BD Biosciences | Cat#553666; RRID: AB_394981 |
| anti-mouse GL7 PE (Clone GL7) | BD Biosciences | Cat#561530; RRID: AB_10715834 |
| anti-mouse Gr-1 PE (Clone RB6-8C5) | BioLegend | Cat#108404; RRID: AB_313369 |
| anti-human HB-EGF (Goat Polyclonal) | R&D Systems | Cat#BAF259; RRID: AB_2114598 |
| anti-mouse I-A/I-E (MHCII) AF647 (Clone M5/114.15.2) | BioLegend | Cat#107618; RRID: AB_493525 |
| anti-mouse I-A/I-E (MHCII) BV711 (Clone M5/114.15.2) | BD Biosciences | Cat#563414; RRID: AB_2738191 |
| anti-mouse I-Ab (MHCII) PE-CF594 (Clone AF6-120.1) | BD Biosciences | Cat#562824; RRID: AB_2737819 |
| anti-mouse IgD BV421 (Clone 11-26c.2a) | BioLegend | Cat#405725; RRID: AB_2562743 |
| anti-mouse IgD BV510 (Clone 11-26c.2a) | BioLegend | Cat#405723; RRID: AB_2562742 |
| anti-mouse Ig κ light chain BV421 (Clone 187.1) | BD Biosciences | Cat#562888; RRID: AB_2737867 |
| anti-mouse Ig λ1, λ2, & λ3 light chain FITC (Clone R26-46) | BD Biosciences | Cat#553434; RRID: AB_394854 |
| anti-mouse/human Ki-67 BV421 (Clone 11F6) | BioLegend | Cat#151208; RRID: AB_2629748 |
| anti-mouse/human Ki-67 BV421 (Clone B56) | BD Biosciences | Cat#562899; RRID: AB_2686897 |
| anti-mouse/human Ki-67 AF647 (Clone B56) | BD Biosciences | Cat#558615; RRID: AB_647130 |
| anti-mouse/human Ki-67 BV650 (Clone B56) | BD Biosciences | Cat#563757; RRID: AB_2688008 |
| anti-mouse Ly6C FITC (Clone AL21) | BD Biosciences | Cat#553104; RRID: AB_394628 |
| anti-RFP (Rabbit Polyclonal) | Rockland | Cat#600-401-379; RRID: AB_2209751 |
| anti-mouse TCRβ FITC (Clone H57-597) | BioLegend | Cat#109205; RRID: AB_313428 |
| anti-mouse TCRβ PE-Cy7 (Clone H57-597) | BioLegend | Cat#109221; RRID: AB_893627 |
| anti-mouse TCRβ BV711 (Clone H57-597) | BD Biosciences | Cat#563135; RRID: AB_2738023 |
| anti-mouse TCR Vβ5.1/5.2 PE (Clone MR9-4) | BD Biosciences | Cat#562086; RRID: AB_394698 |
| anti-mouse Ter-119 Biotin (Clone TER-119) | BioLegend | Cat#116204; RRID: AB_313705 |
| anti-Rabbit IgG (H+L) AF594 (Goat Polyclonal) | Thermo Fisher Scientific | Cat#A-11012; RRID: AB_ 2534079 |
| anti-mouse CD16/CD32 (Mouse BD Fc Block™) | BD Biosciences | Cat#553142; RRID: AB_394656 |
| Chemicals, peptides, and recombinant proteins | ||
| Acetone | Sigma-Aldrich | Cat#179124 |
| Alhydrogel® adjuvant 2% | InvivoGen | Cat#vac-alu-250 |
| Corn oil | Sigma-Aldrich | Cat#PHR2897 |
| Diphtheria Toxin from Corynebacterium diphtheriae | Sigma-Aldrich | Cat#D0564 |
| IgG from rat serum | Sigma-Aldrich | Cat#I4131 |
| Methanol | Sigma-Aldrich | Cat#34860 |
| NP10-HSA (Human Serum Albumin) | Biosearch Technologies | Cat#N-5059-10 |
| NP15-Ova (Ovalbumin) | Biosearch Technologies | Cat#N-5051-100 |
| Ovalbumin | Biosearch Technologies | Cat#O-1000-100 |
| recombinant PA (Protective antigen) | ||
| recombinant HA (A/Solomon Islands/3/2006) | S. Harrison | (Schmidt et al., 2015) |
| 16% Formaldehyde (w/v), Methanol-free | Thermo Fisher Scientific | Cat#28906 |
| Streptavidin AF488 | BioLegend | Cat#405235 |
| Streptavidin PE | BioLegend | Cat#405204 |
| Streptavidin APC | BioLegend | Cat#405207 |
| Streptavidin BV421 | BioLegend | Cat#405225 |
| Streptavidin BV650 | BioLegend | Cat#405232 |
| Sucrose | Sigma-Aldrich | Cat#S9378 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| Tissue-Tek® O.C.T. Compound | Sakura Finetek USA | Cat#4583 |
| Critical commercial assays | ||
| Direct-zol RNA Miniprep | Zymo Research | Cat#R2051 |
| immunoSEQ mouse Tcrβ assay | Adaptive Biotechnologies | https://www.immunoseq.com/assays/ |
| KAPA HyperPlus Kit | Roche Molecular Systems | Cat#07962401001 |
| KAPA Pure Beads | Roche Molecular Systems | Cat#07983280001 |
| LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit | Thermo Fisher Scientific | Cat#L34976 |
| Pan T Cell Isolation Kit II | Miltenyi Biotec | Cat#130-095-130 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific | Cat#Q32851 |
| Qubit RNA IQ Assay | Thermo Fisher Scientific | Cat#Q33222 |
| RNA 6000 Pico kit | Agilent | Cat#5067-1513 |
| SMART-Seq® v4 Ultra Low Input RNA Kit | Takara Bio | Cat#634890 |
| Streptavidin MicroBeads | Miltenyi Biotec | Cat#130-048-101 |
| Transcription Factor Buffer Set | BD Biosciences | Cat#562574 |
| Deposited data | ||
| RNA-seq data | This paper | GSE147035 |
| Tcrβ sequence data | This paper |
https://clients.adaptivebiotech.com/pub/yeh-2021-immunity
DOI: https://dx.doi.org/10.21417/CY2021I |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J (B6) | The Jackson Laboratory | JAX: 000664 |
| Mouse: B6.129S2-H2dlAb1-Ea/J (MHCII−/−) | The Jackson Laboratory | JAX: 003584 |
| Mouse: B6.SJL-Ptprca Pepcb/BoyJ (B6.CD45.1) | The Jackson Laboratory | JAX: 002014 |
| Mouse: B6.Cg-Ptprca Tg(UBC-PA-GFP)1Mnz/J (PAGFP) | The Jackson Laboratory | JAX: 022486 |
| Mouse: B6.Cg-Foxp3tm2Tch/J (FoxP3EGFP) | The Jackson Laboratory | JAX: 006772 |
| Mouse: B6(Cg)-Zbtb46tm1(HBEGF)Mnz/J (zbtb46-DTR) | The Jackson Laboratory | JAX: 019506 |
| Mouse: B6.129S2-Ighmtm1Cgn/J (μMT) | The Jackson Laboratory | JAX: 002288 |
| Mouse: B6.C(Cg)-Cd79atm1(cre)Reth/EhobJ (Mb1Cre) | The Jackson Laboratory | JAX: 020505 |
| Mouse: B6.Cg-Tg(TcraTcrb)425Cbn/J (OT-II Tg) | The Jackson Laboratory | JAX: 004194 |
| Mouse: C57BL/6-Gt(ROSA)26Sortm1(HBEGF)Awai/J (DTRLSL) | The Jackson Laboratory | JAX: 007900 |
| Mouse: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J | The Jackson Laboratory | JAX: 007914 |
| Mouse: Balb/cJ (Balb/c) | The Jackson Laboratory | JAX: 000651 |
| Mouse: C.Cg-Tg(DO11.10)10Dlo/J (DO11.10 Tg) | The Jackson Laboratory | JAX: 003303 |
| Mouse: CByJ.SJL(B6)-Ptprca/J (Balb/c.CD45.1) | The Jackson Laboratory | JAX: 006584 |
| Mouse: Tg(S1pr2-cre/ERT2)#Kuro (S1pr2ERT2Cre) | (Shinnakasu et al., 2016) | MGI: 6435090 |
| Mouse: Ightm2Cgn (B1-8i) | (Sonoda et al., 1997) | MGI:2388486 |
| Mouse: B6.H50Gμ | (Dal Porto et al., 2002) | N/A |
| Software and algorithms | ||
| BD FACSDiva Software | BD Biosciences | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp RRID:SCR_001456 |
| Bioconductor | Huber et al., 2015 | http://www.bioconductor.org/ RRID:SCR_006442 |
| Cytoscape | National Institute of General Medical Sciences | http://cytoscape.org RRID:SCR_003032 |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html RRID:SCR_015687 |
| EnrichmentMap | Merico et al., 2010 | http://baderlab.org/Software/EnrichmentMap RRID:SCR_016052 |
| Fiji (ImageJ) | National Institutes of Health | http://fiji.sc/ RRID: SCR_002285 |
| FlowJo | BD | https://www.flowjo.com/solutions/flowjo RRID:SCR_008520 |
| GraphPad Prism_V9 | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ RRID: SCR_002798 |
| HTSeq tool | European Molecular Biology Laboratory | http://www-huber.embl.de/users/anders/HTSeq/ RRID:SCR_004473 |
| immunoSEQ ANALYZER | Adaptive Biotechnologies (Carlson et al., 2013) | https://clients.adaptivebiotech.com/ |
| STAR RNAseq alignment tool | Dobin et al., 2013 | http://code.google.com/p/rna-star/ RRID:SCR_016533 |
| Trim Galore toolkit | Martin, 2011 | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore RRID:SCR_011847 |