KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Vδ1 APC (TS8.2) | Miltenyi Biotec | Cat#130–100-519 |
| Vδ1 FITC (TS8.2) | Thermo Fisher Scientific | Cat#TCR2730 |
| Vδ2 PE (B6) | BioLegend | Cat#331408 |
| Vδ2 PerCP (B6) | BioLegend | Cat#331410 |
| TCRαβ BV421 (IP26) | BioLegend | Cat#306722 |
| TCRγδ PE (5A6.E9) | Thermo Fisher Scientific | Cat#MHGD04 |
| TCRγδ PE-Cy5 (5A6.E9) | Thermo Fisher Scientific | Cat#MHGD06 |
| CD3 APC (UCHT1) | BioLegend | Cat#300412 |
| CD3 APC-Cy7 (UCHT1) | BioLegend | Cat#300426 |
| CD3 PE-Cy7 (UCHT1) | BioLegend | Cat#300420 |
| CD4 BV786 (SK3) | BD Biosciences | Cat#563877 |
| CD8a BUV496 (RPA-T8) | BD Biosciences | Cat#564804 |
| CD8a BV650 (RPA-T8) | BD Biosciences | Cat#563821 |
| CD45RA BV510 (HI100) | BioLegend | Cat#304142 |
| CCR7 PE-Cy7 (G043H7) | BioLegend | Cat#353226 |
| CD45 BV711 (HI30) | BD Biosciences | Cat#564357 |
| CD103 BUV395 (Ber-ACT8) | BD Biosciences | Cat#564346 |
| CD69 PE-CF594 (FN50) | BD Biosciences | Cat#562617 |
| CD107a BUV395 (H4A3) | BD Biosciences | Cat#565113 |
| NKp44 PE (p44–8) | BD Biosciences | Cat#558563 |
| NKp44 APC (p44–8) | BD Biosciences | Cat#558564 |
| NKp46 PE (9E2) | BioLegend | Cat#331908 |
| NKp46 BV605 (9E2) | BioLegend | Cat#331926 |
| Granzyme B PE (GB12) | Invitrogen | Cat#MHGB04 |
| TNF-α PE-Cy7 (MAb11) | BioLegend | Cat#502930 |
| IFN-γ APC (4S.B3) | eBioscience | Cat#17–7319-82 |
| Nur77 PE (12.4) | eBioscience | Cat#12–5965-82 |
| Purified anti-human TCR γδ (B1) | BioLegend | Cat#331202 |
| Human NKp46/NCR1 (195314) | R&D Systems | Cat#MAB1850 |
| Human NKp44/NCR2 (253415) | R&D Systems | Cat#MAB22491 |
| LEAF Purified Mouse IgG2b, k (MPC-11) | BioLegend | Cat#400323 |
| LEAF Purified Mouse IgG2a, k (MOPC-173) | BioLegend | Cat#400223 |
| Myc-Tag PE (9B11) (αBTNL3) | Cell Signaling Technology | Cat#CST.3739S |
| HA-Tag Alexa Fluor 647 (6E2) (αBTNL8) | Cell Signaling Technology | Cat#CST.3444S |
| Human BTNL8 (2187B) | R&D Systems | Cat#MAB9359–100 |
| Dynabeads™ Human T-Activator CD3/CD28 for T Cell Expansion and Activation | Thermo Fisher Scientific | Cat#11131D |
| Biological Samples | ||
| Fetal Bovine Serum | Biowest | Cat#S01520; Lot#A11504E |
| Human AB Serum | Corning | Cat#35–060-CI; Lot#35060115 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| EDTA, 0.5M, pH8.0 | Corning | Cat#46–034-CI |
| Magnesium Chloride Hexahydrate (MgCl2) | Thermo Fisher Scientific | Cat#BP214–500 |
| Ficoll-Paque PLUS | GE Healthcare Life Sciences | Cat#17–1440-03 |
| RNAlater Stabilization Solution | Ambion | Cat#AM7020 |
| RNAlater RNA Stabilization Reagent | QIAGEN | Cat#76104 |
| 2-Mercaptoethanol (BME) | Sigma-Aldrich | Cat#M7154 |
| Phorbol Myristate Acetate | Sigma-Aldrich | Cat#P1585 |
| Ionomycin Calcium Salt from Streptomyces conglobatus | Sigma-Aldrich | Cat#10634 |
| BD GolgiPlug Protein Transport Inhibitor | BD Biosciences | Cat#555029 |
| BD GolgiStop Protein Transport Inhibitor | BD Biosciences | Cat#554724 |
| Recombinant Human IL-2 | NIH AIDS Reagent Program | Cat#136 |
| Recombinant Human IL-15 (carrier-free) | BioLegend | Cat#570304 |
| Critical Commercial Assays | ||
| S.O.C. Medium | Thermo Fisher Scientific | Cat#15544034 |
| Triton X-100 | Sigma-Aldrich | Cat#T9284 |
| Nuclease-free Water | Ambion | Cat#AM9932 |
| Recombinant RNase Inhibitor (25,000 units) | Clontech | Cat#2313B |
| 5M Betaine Solution | Sigma-Aldrich | Cat#B0300–1VL |
| 1M MgCl2 | Thermo Fisher Scientific | Cat#AM9530G |
| Ethanol 200 Proof | Decon Labs Inc | Cat#DSP-MD 43 |
| Buffer EB | QIAGEN | Cat#19086 |
| Critical Commercial Assays | ||
| LIVE/DEAD® Fixable Aqua Dead Cell Stain Kit | Thermo Fisher Scientific | Cat#L34966 |
| LIVE/DEAD® Fixable Near-IR Dead Cell Stain Kit | Thermo Fisher Scientific | Cat#L34975 |
| BD Cytofix/Cytoperm Plus Fixation/Permeabilization Solution Kit | BD Biosciences | Cat#554714 |
| AllPrep DNA/RNA/Protein Mini Kit | QIAGEN | Cat#80004 |
| GoScript Reverse Transcriptase Kit | Promega | Cat#A5001 |
| SYBR Advantage qPCR Premix | Clontech | Cat#639676 |
| μMACS mRNA Isolation Kit | Miltenyi Biotec | Cat#130–075-201 |
| SMARTer® RACE 5′/3′ Kit (contains NucleoSpin Gel and PCR Clean-Up Kit) | Clontech | Cat#634859 |
| SuperScript II Reverse Transcriptase | Thermo Fisher Scientific | Cat#18064014 |
| RNaseOUT Recombinant Ribonuclease Inhibitor | Thermo Fisher Scientific | Cat#10777019 |
| SYBR Gold Nucleic Acid Gel Stain | Thermo Fisher Scientific | Cat#S-11494 |
| TOPO TA Cloning Kit for Sequencing with One Shot® MAX Efficiency DH5α-T1R E. coli | Thermo Fisher Scientific | Cat#K459540 |
| SYBR® Safe DNA Gel Stain | Thermo Fisher Scientific | Cat#S33102 |
| TrackIt Cyan/Orange Loading Buffer | Thermo Fisher Scientific | Cat#10482–028 |
| GeneRuler 1kb DNA Ladder (ready-to-use) | Thermo Fisher Scientific | Cat#SM0313 |
| PrimeScript Reverse Transcriptase | Clontech | Cat#2680A |
| KAPA HiFi HotStart ReadyMix | Kapa Biosystems | Cat#KK2602 |
| Agilent High Sensitivity DNA Kit | Agilent | Cat#5067–4626 |
| Nextera XT DNA Sample Preparation Kit (96 samples) | Illumina | Cat#FC-131–1096 |
| Nextera XT Index Kit (96 indices, 384 samples) | Illumina | Cat#FC-131–1002 |
| Epitope Retrieval Solution 2 BOND | Leica Biosystems | Cat#AR9640 |
| Bond Polymer Refine Detection | Leica Biosystems | Cat#DS9800 |
| Deposited Data | ||
| RNA-seq from Vδ1+ IELs | GEO Database | GEO: GSE123649 |
| Experimental Models: Cell Lines | ||
| HEK293T (ATCC 293T) | American Type Culture Collection | Cat#CRL-3216 |
| SKW-3 | German Collection of Microorganisms and Cell Cultures | Cat#ACC 53 |
| Oligonucleotides | ||
|
GAPDH Primers: Forward: 5′-ATGGGGAAGGTGAAGGTCG-3′ Reverse: 5′-GGGGTCATTGATGGCAACAATA-3′ |
This paper | N/A |
|
BTNL3 Primers: Forward: 5′-TCAGTTTCTACGAGCTGGTGTC-3′ Reverse: 5′-CCAAGGCCTGGACAAACTT-3′ |
Lebrero-Fernández et al., 2016 | N/A |
|
BTNL8 Primers: Forward: 5′-GCTCTCATGCTCAGTTTGGTT-3′ Reverse: 5′-GTCTGGCCCAAACACCTG-3′ |
Lebrero-Fernández et al., 2016 | N/A |
| 10mM dNTP Mix | Thermo Fisher Scientific | Cat#18427013 |
| OligoDT-5′Biotinylated: 5′-Biot-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′ |
Picelli et al., 2014 | N/A |
| 100mM dATP | Roche | Cat#11934511001 |
| 100mM dCTP | Roche | Cat#11934520001 |
| 100mM dGTP | Roche | Cat#11934538001 |
| 100mM dTTP | Roche | Cat#11934546001 |
| TSO-5′Biotinylated: 5′-Biot-AAGCAGTGGTATCAACGCAGAGTA CATrGrG+G-3′ |
Picelli et al., 2014 | N/A |
| ISPCR-5′Biotinylated: 5′-Biot-AAGCAGTGGTATCAACGCAGAGT-3′ |
Picelli et al., 2014 | N/A |
| Recombinant DNA | ||
| pMIG II (pMSCV-IRES-GFP II) | Holst et al., 2006 | N/A |
| cDNA: BTNL3 (GenBank: NM_197975.2), BTNL8 (GenBank: NM_001040462.2) | Genscript | N/A |
| cDNA: Control 94 and 95, Active 46 and 81, γδTCRs | Integrated DNA Technologies | N/A |
| cDNA: TRDC-P2A-TRGC | Integrated DNA Technologies | N/A |
| Software and Algorithms | ||
| FlowJo (version 10.2) | FlowJo | https://www.flowjo.com/solutions/flowjo/downloads |
| R (version 3.4.0) | R | https://cran.r-project.org |
| RStudio (version 1.0.143) | RStudio | https://www.rstudio.com/products/rstudio/download2/ |
| iceLogo | Colaert et al., 2009 | https://iomics.ugent.be/icelogoserver/ |
| Diva 8 | BD Biosciences | http://www.bdbiosciences.com |
| Sequencher (version 5.2.3) | Gene Codes Corporation | http://www.genecodes.com/sequencher |
| IMGT | IMGT®, the international ImMunoGeneTics information system | http://www.imgt.org |
| PLINK (version 1.9) | PLINK | https://www.cog-genomics.org/plink2 |
| edgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| limma | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Trim Galore (version 0.4.4) | Krueger n.d. | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| kallisto (version 0.43.0) | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| Other | ||
| Zirconium Oxide Beads 0.5mm RNase Free | Next Advance | SKU#ZROB05-RNA |
| Zirconium Oxide Beads 1.0mm RNase Free | Next Advance | SKU#ZROB10-RNA |
| Corning 96-Well Clear Flat Bottom Polystyrene Not Treated Microplate | Corning | Cat#3370 |
| Hard-Shell 96-Well PCR Plates (thin-wall) | Bio-Rad | Cat#HSP9631 |
| Microseal ‘F’ Foil Seals | Bio-Rad | Cat#MSF1001 |
| RT-LTS-A-10uL-/F-960/10 Tips | Rainin | Cat#30389225 |
| RT-LTS-A-200uL-/F-960/10 Tips | Rainin | Cat#30389239 |
| Invitrogen Magnetic Stand-96 | Thermo Fisher Scientific | Cat#AM10027 |