KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Live/Dead viability dye | Invitrogen | Cat# L34976 |
| Mouse anti-pig CD3ε antibody | BD | Clone BB23-8E6-8C8 |
| Anti-JAML antibody | Abcam | Clone EPR15289 |
| Alexa Fluor 488-conjugated anti-rabbit IgG secondary antibody | Abcam | Cat# ab150077; RRID: AB_2630356 |
| Mouse anti-pig TCRδ antibody | WSU mAb Center | Clone PGBL22A |
| Biological samples | ||
| Pig thymus | University of Florida’s Animal Sciences Department | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Mouse CD1d (mCD1d) tetramer | National Institutes of Health Tetramer Core Facility | N/A |
| Critical commercial assays | ||
| Chromium Next GEM Single Cell 3′ reagent kit | 10xGenomics | RRID: SCR_019145 |
| NovaSeq 6000 sequencer | Illumina | RRID: SCR_019152 |
| Deposited data | ||
| Raw data | This paper | GSE192520 |
| Human thymus dataset | Le et al. (2020) | GSE139042 |
| Mouse thymic iNKT cell dataset | Harsha Krovi et al. (2020) | GSE152786 |
| Software and algorithms | ||
| Cell Ranger v3.1 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| R (4.0.2) | CRAN | https://www.r-project.org/ |
| Seurat (v3.2.2) | Stuart et al. (2019) | https://satijalab.org/seurat/ |
| EnhancedVolcano | Blighe et al. (2018) | https://github.com/kevinblighe/EnhancedVolcano |
| Monocle 3 | Cao et al. (2019); Levine et al. (2015); Traag et al., 2019; Trapnell et al. (2014) | https://cole-trapnell-lab.github.io/monocle3/ |
| SCORPIUS (1.0.8) | Cannoodt et al. (2016) | https://github.com/rcannood/SCORPIUS |
| Slingshot (2.0.0) | Street et al. (2010) | https://bioconductor.org/packages/release/bioc/vignettes/slingshot/inst/doc/vignette.html |
| FlowJo v10 | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo |
| BioRender | https://biorender.com/ | RRID:SCR_018361 |
| Custom scripts | This paper | https://doi.org/10.5281/zenodo.6609557 |