An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

MAIT/TRDV2+ gdT

Ontology Term: mucosal invariant T cellCL:0000940
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: mucosal invariant T-cell / TRDV2+ gamma-delta T cells, mucosal invariant T lymphocyte / TRDV2+ gamma-delta T cells, mucosal invariant T-lymphocyte / TRDV2+ gamma-delta T cells
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KLRB1, TRDC, TRGC1, TRGC2, IL18RAP, CEBPD, ZBTB16, RORA, CCR6, IL23R
Canonical Marker Genes: KLRB1, TRDC, TRGC1, TRGC2, IL18RAP, CEBPD, ZBTB16, RORA, CCR6, IL23R
Rationale: This cluster is a mix of MAIT cells (KLRB1, SLC4A10, ZBTB16, IL23R, IL18R1, CEPBD, CCR6, DPP4) and Vδ2Vγ9+ γδ T cells (TRDV2, TRDC, TRGC1, TRGC2, ZBTB16, KLRB1, IL18R1, DPP4) which share a similar phenotype and transcriptional profile (Provine et al., 2018; Wragg et al., 2020).
Rationale DOI: 10.3389/fimmu.2018.00756 10.1016/j.celrep.2020.107773 10.1038/s41590-023-01575-1

Set of Labels Description: The annotation provided in this first version comprises 42 categories that provide a stable categories to classify single-cell transcriptomes of SLOs, useful for tools like Azimuth (see external URLs). In the next version, we will add a more detailed classification, encompassing all cell types and states identified in the tonsil atlas. A validation cohort was included to confirm the presence and accuracy of each annotation this latter level, using criteria such as cell neighborhood preservation, conservation of bona fide marker genes, and annotation confidence derived from the KNN classifier. For a full description and interpretation of this validation cohort, please refer to the final section of the manuscript.
Annotation Method: manual

Ontology Term: mucosal invariant T cellCL:0000940
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: mucosal invariant T-cell / TRDV2+ gamma-delta T cells, mucosal invariant T lymphocyte / TRDV2+ gamma-delta T cells, mucosal invariant T-lymphocyte / TRDV2+ gamma-delta T cells
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KLRB1, TRDC, TRGC1, TRGC2, IL18RAP, CEBPD, ZBTB16, RORA, CCR6, IL23R
Canonical Marker Genes: KLRB1, TRDC, TRGC1, TRGC2, IL18RAP, CEBPD, ZBTB16, RORA, CCR6, IL23R
Rationale: This cluster is a mix of MAIT cells (KLRB1, SLC4A10, ZBTB16, IL23R, IL18R1, CEPBD, CCR6, DPP4) and Vδ2Vγ9+ γδ T cells (TRDV2, TRDC, TRGC1, TRGC2, ZBTB16, KLRB1, IL18R1, DPP4) which share a similar phenotype and transcriptional profile (Provine et al., 2018; Wragg et al., 2020).
Rationale DOI: 10.3389/fimmu.2018.00756 10.1016/j.celrep.2020.107773 10.1038/s41590-023-01575-1

Set of Labels Description: The annotation provided in this first version comprises 42 categories that provide a stable categories to classify single-cell transcriptomes of SLOs, useful for tools like Azimuth (see external URLs). In the next version, we will add a more detailed classification, encompassing all cell types and states identified in the tonsil atlas. A validation cohort was included to confirm the presence and accuracy of each annotation this latter level, using criteria such as cell neighborhood preservation, conservation of bona fide marker genes, and annotation confidence derived from the KNN classifier. For a full description and interpretation of this validation cohort, please refer to the final section of the manuscript.
Annotation Method: manual