An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD8 T

Full Name: CD8 T cell
Closest Ontology Term: CD8-positive, alpha-beta cytotoxic T cellCL:0000794
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD8-positive, alpha-beta cytotoxic T-lymphocyte, cytotoxic T cell, killer T-cell, killer T lymphocyte, killer T cell, cytotoxic T lymphocyte, CD8-positive, alpha-beta cytotoxic T lymphocyte, killer T-lymphocyte, cytotoxic T-lymphocyte, cytotoxic T-cell, CD8-positive, alpha-beta cytotoxic 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.: CD3D, CD3G, CD8A, CD8B, CCL5, GZMK, NKG7, KLRG1, PRF1, KLRK1,
Canonical Marker Genes: CD3D, CD3G, CD8A, CD8B, CCL5, GZMK, NKG7, KLRG1, PRF1, KLRK1
Rationale: This is a cluster of non-naive, non-central memory CD8 T cells. It is rather a broad annotation, which in version 2.0 we will split into resident memory CD8 T, resident memory activated T, effector memory CD8 T, CD8 T follicular, DC-recruiter CD8 T, and IFN+ CD8 T cells, in line with figure 3 of our paper.
Rationale DOI: 10.1002/eji.201343751

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

Full Name: CD8 T cell
Closest Ontology Term: CD8-positive, alpha-beta cytotoxic T cellCL:0000794
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD8-positive, alpha-beta cytotoxic T-lymphocyte, cytotoxic T cell, killer T-cell, killer T lymphocyte, killer T cell, cytotoxic T lymphocyte, CD8-positive, alpha-beta cytotoxic T lymphocyte, killer T-lymphocyte, cytotoxic T-lymphocyte, cytotoxic T-cell, CD8-positive, alpha-beta cytotoxic 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.: CD3D, CD3G, CD8A, CD8B, CCL5, GZMK, NKG7, KLRG1, PRF1, KLRK1,
Canonical Marker Genes: CD3D, CD3G, CD8A, CD8B, CCL5, GZMK, NKG7, KLRG1, PRF1, KLRK1
Rationale: This is a cluster of non-naive, non-central memory CD8 T cells. It is rather a broad annotation, which in version 2.0 we will split into resident memory CD8 T, resident memory activated T, effector memory CD8 T, CD8 T follicular, DC-recruiter CD8 T, and IFN+ CD8 T cells, in line with figure 3 of our paper.
Rationale DOI: 10.1002/eji.201343751

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