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

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Cell Metadata

HLA-DRhi_ILC3

Ontology Term: group 3 innate lymphoid cellCL:0001071
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.: group 3 innate lymphoid cellCL:0001071
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DRA, KIT, RORC, IL23R, SGIP1
Canonical Marker Genes: KIT, IL7R, CCR6, IL23R, AHR, RORC,
Rationale: Top differential gene expression mapped most with NKp44- ILC3 in Azimuth tonsil dataset, high expression of HLA-DR and subpopulation of ILC3 with high HLA-DR has been described (see DOI)
Rationale DOI: https://doi.org/10.1038/ni.3368; DOI: 10.1016/j.celrep.2017.09.070

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: group 3 innate lymphoid cellCL:0001071
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.: group 3 innate lymphoid cellCL:0001071
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: HLA-DRA, KIT, RORC, IL23R, SGIP1
Canonical Marker Genes: KIT, IL7R, CCR6, IL23R, AHR, RORC,
Rationale: Top differential gene expression mapped most with NKp44- ILC3 in Azimuth tonsil dataset, high expression of HLA-DR and subpopulation of ILC3 with high HLA-DR has been described (see DOI)
Rationale DOI: https://doi.org/10.1038/ni.3368; DOI: 10.1016/j.celrep.2017.09.070

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