An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 naive

Full Name: naive CD4 T cell
Closest Ontology Term: naive T cellCL:0000898
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: naive T lymphocyte, naive T-lymphocyte, naive T-cell, CD4 naive 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, CD3E, CD3G, LEF1, CCR7, NOSIP, SELL, BACH2
Canonical Marker Genes: CD3D, CD3E, CD3G, LEF1, CCR7, NOSIP, SELL, BACH2
Rationale: Cluster of naive (antigen-inexperienced) CD4+ T cells that expresses canonical markers of T cells (CD3D, CD3E, CD3G), markers of homing into the T cell zone of secondary lymphoid organs (CCR7), and markers typical of naive T cells (SELL, LEF1). At the protein level, these cells expressed CD45RA.
Rationale DOI: 10.1038/s41467-020-15543-y 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: naive CD4 T cell
Closest Ontology Term: naive T cellCL:0000898
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: naive T lymphocyte, naive T-lymphocyte, naive T-cell, CD4 naive 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, CD3E, CD3G, LEF1, CCR7, NOSIP, SELL, BACH2
Canonical Marker Genes: CD3D, CD3E, CD3G, LEF1, CCR7, NOSIP, SELL, BACH2
Rationale: Cluster of naive (antigen-inexperienced) CD4+ T cells that expresses canonical markers of T cells (CD3D, CD3E, CD3G), markers of homing into the T cell zone of secondary lymphoid organs (CCR7), and markers typical of naive T cells (SELL, LEF1). At the protein level, these cells expressed CD45RA.
Rationale DOI: 10.1038/s41467-020-15543-y 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