An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

dnT

Ontology Term: double negative thymocyteCL:0002489
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD4-CD8- T cell, double negative T cell
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3G, CD3D, CD3E, HAVCR2, GPR183, ISG20
Canonical Marker Genes: CD3G, CD3D, CD3E, HAVCR2, GPR183, ISG20
Rationale: Double negative T cells express the αβ T cell receptor but do not express CD4, CD8, or natural killer cell markers. This cluster had a profile of inflammatory and activated DN T cells expressing HLA-DRB1, HLA-DPA1, CD38 and GPR183.
Rationale DOI: 10.3389/fimmu.2022.816005 10.1126/sciimmunol.abe6291

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: double negative thymocyteCL:0002489
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD4-CD8- T cell, double negative T cell
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3G, CD3D, CD3E, HAVCR2, GPR183, ISG20
Canonical Marker Genes: CD3G, CD3D, CD3E, HAVCR2, GPR183, ISG20
Rationale: Double negative T cells express the αβ T cell receptor but do not express CD4, CD8, or natural killer cell markers. This cluster had a profile of inflammatory and activated DN T cells expressing HLA-DRB1, HLA-DPA1, CD38 and GPR183.
Rationale DOI: 10.3389/fimmu.2022.816005 10.1126/sciimmunol.abe6291

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