Human lymph node slices cultured with and without ex vivo stimulation by liposomal TLR4 and QS-21 adjuvant

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Cell Metadata

CD16low_NK_cells

Ontology Term: mature natural killer cellCL:0000824
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: natural killer cellCL:0000623
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NCAM1, KRLF1, NKG7, KLRD1, EOMES, KLRB1
Canonical Marker Genes: NCAM1, KRLF1, EOMES
Rationale: This cell type was annotated as a natural killer cell by canonical gene expression, but displayed lower CD16 expression than the other natural killer cell subset within the dataset. Similar transcript levels of NCAM1 between two subsets also suggest that ontology term CL:0000938 would not be more appropriate in this case. Standard accepted NK subsets, and described in tonsil Azimuth dataset.
Rationale DOI: 10.1016/j.immuni.2024.01.006

Set of Labels Description: Cell annotations were based on the finest possible label to describe the 18 clusters found across both culture conditions (control and stimulated) following integration and clustering. Gene expression across clusters correlated with matched cell annotations in the uncultured, whole lymph node dataset (LN partial T and B cell depletion) in addition to some culture-specific cell clusters
Annotation Method: manual

Ontology Term: mature natural killer cellCL:0000824
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: natural killer cellCL:0000623
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: NCAM1, KRLF1, NKG7, KLRD1, EOMES, KLRB1
Canonical Marker Genes: NCAM1, KRLF1, EOMES
Rationale: This cell type was annotated as a natural killer cell by canonical gene expression, but displayed lower CD16 expression than the other natural killer cell subset within the dataset. Similar transcript levels of NCAM1 between two subsets also suggest that ontology term CL:0000938 would not be more appropriate in this case. Standard accepted NK subsets, and described in tonsil Azimuth dataset.
Rationale DOI: 10.1016/j.immuni.2024.01.006

Set of Labels Description: Cell annotations were based on the finest possible label to describe the 18 clusters found across both culture conditions (control and stimulated) following integration and clustering. Gene expression across clusters correlated with matched cell annotations in the uncultured, whole lymph node dataset (LN partial T and B cell depletion) in addition to some culture-specific cell clusters
Annotation Method: manual