An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

NK_CD56bright

Ontology Term: CD16-negative, CD56-bright natural killer cell, humanCL:0000938
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD56-bright cytokine secreting NK cell, CD16-negative, CD56-bright NK cell, CD16-CD56bright NK cell, CD56-bright cytokine secreting natural killer cell
CategoryClass of which the cell type is a subclass.: natural killer cellCL:0000623
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KLRF1, GNLY, KLRD1, NKG7, NCAM1, EOMES, AREG
Canonical Marker Genes: KLRF1, GNLY, KLRD1, NKG7, NCAM1, EOMES, AREG
Rationale: These cells have an immunoregulatory function, possess a strong ability to react to cytokine stimulation, are mainly found in secondary lymphoid organs, and have limited cytotoxic capacity. They are the precursors of CD16+CD56- NK cells.
Rationale DOI: 10.1002/cyto.b.21162 10.3389/fimmu.2020.00812 10.1101/630657

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: CD16-negative, CD56-bright natural killer cell, humanCL:0000938
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD56-bright cytokine secreting NK cell, CD16-negative, CD56-bright NK cell, CD16-CD56bright NK cell, CD56-bright cytokine secreting natural killer cell
CategoryClass of which the cell type is a subclass.: natural killer cellCL:0000623
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KLRF1, GNLY, KLRD1, NKG7, NCAM1, EOMES, AREG
Canonical Marker Genes: KLRF1, GNLY, KLRD1, NKG7, NCAM1, EOMES, AREG
Rationale: These cells have an immunoregulatory function, possess a strong ability to react to cytokine stimulation, are mainly found in secondary lymphoid organs, and have limited cytotoxic capacity. They are the precursors of CD16+CD56- NK cells.
Rationale DOI: 10.1002/cyto.b.21162 10.3389/fimmu.2020.00812 10.1101/630657

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