An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

NK

Ontology Term: natural killer cellCL:0000623
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: large granular lymphocyte, NK cell, null 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, KLRD1, KLRK1, NKG7, GNLY, FCGR3A, PRF1, CCL5, CX3CR1, GZMA, TBX21
Canonical Marker Genes: KLRF1, KLRD1, KLRK1, NKG7, GNLY, FCGR3A, PRF1, CCL5, CX3CR1, GZMA, TBX21
Rationale: Fully differentiated CD16+ NK cells with high cytotoxic capacity.
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: natural killer cellCL:0000623
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: large granular lymphocyte, NK cell, null 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, KLRD1, KLRK1, NKG7, GNLY, FCGR3A, PRF1, CCL5, CX3CR1, GZMA, TBX21
Canonical Marker Genes: KLRF1, KLRD1, KLRK1, NKG7, GNLY, FCGR3A, PRF1, CCL5, CX3CR1, GZMA, TBX21
Rationale: Fully differentiated CD16+ NK cells with high cytotoxic capacity.
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