REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Bcl6 Alexa Fluor 647 conjugated (clone: IG191E/A8)	BioLegend	Cat# 648306; RRID: AB_2565299
Mouse monoclonal anti-CD3 Alexa Fluor 700 conjugated (clone: SP34-2)	BD Biosciences	Cat# 557917; RRID: AB_396938
Mouse monoclonal anti-CD3 BUV805 conjugated (clone: SP34-2)	BD Biosciences	Cat# 742053; RRID: AB_2871342
Mouse monoclonal anti-CD20 BUV805 conjugated (clone: 2H7)	BD Biosciences	Cat# 612905; RRID: AB_2870192
Mouse monoclonal anti-CD20 BV510 conjugated (clone: 2H7)	BD Biosciences	Cat# 563067; RRID: AB_2737985
Mouse monoclonal anti-CD20 PE-CF594 conjugated (clone: 2H7)	BD Biosciences	Cat# 562295; RRID: AB_11153322
Mouse monoclonal anti-CD26 unconjugated (clone: clone5)	In house	N/A
Mouse monoclonal anti-CD28 BV711 conjugated (clone: CD28.2)	BD Biosciences	Cat# 563131; RRID: AB_2738020
Mouse monoclonal anti-CD45 BUV395 conjugated (clone: D058-1283)	BD Biosciences	Cat# 564099; RRID: AB_2738591
Mouse monoclonal anti-CD45 PE-Cy7 conjugated (clone: D058-1283)	BD Biosciences	Cat# 561294; RRID: AB_10612014
Mouse monoclonal anti-CD69 APC/Fire 750 conjugated (clone: FN50)	BioLegend	Cat# 310946; RRID: AB_2616709
Mouse monoclonal anti-CD94 APC conjugated (clone: HP-3D9)	BD Biosciences	Cat# 559876; RRID: AB_398679
Mouse monoclonal anti-CD95 BUV737 conjugated (clone: DX2)	BD Biosciences	Cat# 612790; RRID: AB_2870117
Mouse monoclonal anti-CD95 PE-Cy7 conjugated (clone: DX2)	BD Biosciences	Cat# 561633; RRID: AB_10894384
Mouse monoclonal anti-CD159a (NKG2A) APC conjugated (clone: Z199)	Beckman Coulter	Cat# A60797; RRID: AB_10643105
Mouse monoclonal anti-CD183 (CXCR3) Alexa Fluor 647 conjugated (clone: G025H7)	BioLegend	Cat# 353712; RRID: AB_10962948
Mouse monoclonal anti-CD183 (CXCR3) Alexa Fluor 700 conjugated (clone: G025H7)	BioLegend	Cat# 353742; RRID: AB_2616920
Mouse monoclonal anti-CD183 (CXCR3) PE-Dazzle594 (clone: G025H7)	BioLegend	Cat# 353736; RRID:AB_2564288
Mouse monoclonal anti-CD185 (CXCR5) PE-eFluor610 conjugated (clone: MU5UBEE)	Thermo Fisher Scientific	Cat# 61-9185-42; RRID: AB_2574677
Rat monoclonal anti-CD195 (CCR5) BV421 conjugated (clone: J418F1)	BioLegend	Cat# 359118; RRID: AB_2563577
Mouse monoclonal anti-CD196 (CCR6) BV785 conjugated (clone: G034E3)	BioLegend	Cat# 353422; RRID: AB_2563660
Mouse monoclonal anti-CD218 (IL-18Rα) PE-Vio770 conjugated (clone: H44)	Miltenyi Biotec	Cat# 130-101-723; RRID: AB_2656352
Mouse monoclonal anti-CD226 (DNAM-1) BV605 conjugated (clone: 11A8)	BioLegend	Cat# 338324; RRID: AB_2721543
Mouse monoclonal anti-CD326 (Ep-CAM) PE-CF594 conjugated (clone: EBA-1)	BD Biosciences	Cat# 565399; RRID: AB_2739219
Mouse monoclonal anti-eomes PerCP-eFluor710 conjugated (clone: WD1928)	Thermo Fisher Scientific	Cat# 46-4877-42; RRID: AB_2573759
Rat monoclonal anti-GM-CSF BV421 conjugated (clone: BVD2-21C11)	BD Biosciences	Cat# 562930; RRID: AB_2737899
Mouse monoclonal anti-granzyme B BV510 conjugated (clone: GB11)	BD Biosciences	Cat# 563388; RRID: AB_2738174
Mouse monoclonal anti-IFNγ BUV395 conjugated (clone: B27)	BD Biosciences	Cat# 563563; RRID: AB_2738277
Mouse monoclonal anti-IL-17A BV605 conjugated (clone: BL168)	BioLegend	Cat# 512326; RRID: AB_2563887
Mouse monoclonal anti-PLZF PE-CF594 conjugated (clone: R17-809)	BD Biosciences	Cat# 565738; RRID: AB_2739339
Mouse monoclonal anti-T-bet BV421 conjugated (clone: 4B10)	BioLegend	Cat# 644816; RRID: AB_10959653
Mouse monoclonal anti-TCR Vδ1 PE-Cy7 conjugated (clone: TS8.2)	Thermo Fisher Scientific	Cat# 25-5679-42; RRID: AB_2762454
Mouse monoclonal anti-TCR Vδ2 FITC conjugated (clone: 15D)	Thermo Fisher Scientific	Cat# TCR2732; RRID:AB_417095
Mouse monoclonal anti-TCR Vδ2 unconjugated (clone: 15D)	Thermo Fisher Scientific	Cat# TCR1732; RRID: AB_417090
Mouse monoclonal anti-TCR Vγ9 FITC conjugated (clone: 7A5)	Thermo Fisher Scientific	Cat# TCR2720; RRID: AB_417094
Mouse monoclonal anti-TNFα APC-Cy7 conjugated (clone: MAb11)	BioLegend	Cat# 502944; RRID: AB_2562870
Goat polyclonal anti-mouse IgG (H + L) cross-adsorbed secondary PE conjugated	Thermo Fisher Scientific	Cat# P-852; RRID: AB_2539848
Biological samples
Healthy human whole blood	University of Melbourne, Department of Microbiology and Immunology	N/A
Chemicals, peptides, and recombinant proteins
Anti-PE MicroBeads	Miltenyi Biotec	Cat# 130-048-801
Cytofix	BD Biosciences	Cat# 554655
Cytofix/cytoperm kit	BD Biosciences	Cat# 554714
dNTP mix	Meridian Bioscience	Cat# BIO-39053
(E)-1-Hydroxy-2-methyl-2-butenyl 4-pyrophosphate lithium salt (HMB-PP)	Sigma Aldrich	Cat# 95098; CAS# 396726-03-7
Ficoll-Paque Plus	Sigma Aldrich	Cat# GE17-1440-03
GolgiPlug	BD Biosciences	Cat# 555029
GolgiStop	BD Biosciences	Cat# 554724
Igepal	Sigma Aldrich	Cat# I8896; CAS# 9002-93-1
Ionomycin	Sigma Aldrich	Cat# 13909; EC# 200-664-3
Isopentenyl pyrophosphate trilithium salt (IPP)	Sigma Aldrich	Cat# 00297; CAS# 18687-43-9
Live/dead fixable aqua dead cell stain	Thermo Fisher Scientific	Cat# L34957
Live/dead fixable blue dead cell stain	Thermo Fisher Scientific	Cat# L34962
Live/dead fixable green dead cell stain	Thermo Fisher Scientific	Cat# L34970
Phorbol 12-Myristate 13-Acetate	Abcam	CAT# ab120297; CAS# 16561-29-8
Random hexamer primer	Meridian Bioscience	Cat# BIO-38028
Recombinant human IL-2	Peprotech	Cat# 200-02; Accession# P60568
Recombinant rhesus macaque IL-12	R and D Systems	Cat# 3216-RL-025; Accession# P48095 and NP_001038199
Recombinant rhesus macaque IL-18	R and D Systems	Cat# 2548-RM-025; Accession# AAK13416
RNasin Plus Ribonuclease Inhibitor	Promega	Cat# N2615
Streptavidin PE-TR	Thermo Fisher Scientific	Cat# SA1017
SYBR Safe DNA gel stain	Thermo Fisher Scientific	Cat# S33102
Transcription buffer staining kit	BD Biosciences	Cat# 562574
Zoledronic acid monohydrate (Zol)	Sigma Aldrich	Cat# SML0223; CAS# 165800-06-6
Critical commercial assays
Biotinylation Kit / Biotin Conjugation Kit (Fast, Type A)	Abcam	Cat# ab201795
HotStarTaq Plus DNA Polymerase	Qiagen	Cat# 203609
SuperScript III Reverse Transcriptase	Thermo Fisher Scientific	Cat# 18080044
Deposited data
Aligned, single-cell TCRG/TCRD sequences	This paper	Mendeley Data: https://doi.org/10.17632/bpwtp95rpw.1
Experimental models: Organisms/strains
Pigtail macaques (Macaca nemestrina)	Australian National Macaque Breeding Colony	N/A
Oligonucleotides
CAT CTA TGG CCC TGG TTT CA	Integrated DNA Technologies	Rakasz et al.88; Fwd, macTCRDV2- External
TGG CAG TCA AGA GAA AAT TG	Integrated DNA Technologies	Rakasz et al.88; Rev, macTCRDC- External
AGA CCT GGT GAA GTC ATA C	Integrated DNA Technologies	Rakasz et al.88; Fwd, macTCRGV9- External
GTT GCT CTT CTT TTC TTG CC	Integrated DNA Technologies	Rakasz et al.88; Rev, macTCRGC- External
CAG AGA GAG ATG AAG GGT CTT AC	Integrated DNA Technologies	Fwd, macTCRDV2- Internal
CAC TGG GAG AGA CGA CAA TAG	Integrated DNA Technologies	Rev, macTCRDC- Internal
CCT GGT GAA GTC ATA CAG TTC C	Integrated DNA Technologies	macTCRGV9- Internal
AAT AGT GGG CTT GGG TGA AAT A	Integrated DNA Technologies	macTCRGC- Internal
Software and algorithms
Code for TCR sequence processing and analysis	This paper	GitHub: https://github.com/BarberAxthelm/Vd2-Vg9_TCR_Analysis
BD FACSDiva	BD Biosciences	N/A
Biorender	Biorender	https://biorender.com/
FlowJo (v10.8.1)	FlowJo, LLC, BD Biosciences	https://www.flowjo.com/
MiXCR (v3.0.13)	Bolotin et al.89	https://docs.milaboratories.com/
Prism (v9.4.1)	GraphPad	https://www.graphpad.com/scientific-software/prism/
RStudio (v4.1.3)	RStudio, PBC	https://www.rstudio.com/
circlize (v0.4.15)	Gu et al.90	https://jokergoo.github.io/circlize_book/book/
ggalluvial (v0.12.3)	Brunson91	https://corybrunson.github.io/ggalluvial/
msa (v1.26.0)	Bodenhofer et al.92	http://bioconductor.org/packages/release/bioc/html/msa.html
Parallel	R Core Team93	https://www.R-project.org/
Tidyverse (v1.3.1)	Wickham et al.94	https://www.tidyverse.org/
UpSetR (v1.4.0)	Conway et al.95	https://cran.r-project.org/web/packages/UpSetR/index.html
vegan (v2.6-2)	Jari Oksanen, et al.96	https://CRAN.R-project.org/package=vegan
Other
BD FACSAria III cell sorter	BD Biosciences	N/A
BD LSRFortessa cell analyzer	BD Biosciences	N/A
CELL-DYN Emerald Hematology Analyzer	Abbott Laboratories	N/A