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

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Cell Metadata

SELL+ID2hi ILC

Ontology Term: CD34-negative, CD117-positive innate lymphoid cell, humanCL:0001072
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.: immature innate lymphoid cellCL:0001082
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: SELL, ID2, IL7R, KLRB1, IL4I1, , CD200R1, XCL2, XCL1, LINC00299, KIT
Canonical Marker Genes: IL7R, KLRB1, KIT
Rationale: Top differential gene expression mapped most with ILC1 in Azimuth tonsil dataset, including some NCAM1, NCR1, EOMES however also some expression of IL23R, RORC, AHR characteristic of ILC3, and GATA3 characteristic of ILC2. Had highest expression of SELL and ID2 in the ILCs which has been associated with more naive ILCs (see DOI)
Rationale DOI: https://doi.org/10.1038/ni.3368

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: CD34-negative, CD117-positive innate lymphoid cell, humanCL:0001072
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.: immature innate lymphoid cellCL:0001082
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: SELL, ID2, IL7R, KLRB1, IL4I1, , CD200R1, XCL2, XCL1, LINC00299, KIT
Canonical Marker Genes: IL7R, KLRB1, KIT
Rationale: Top differential gene expression mapped most with ILC1 in Azimuth tonsil dataset, including some NCAM1, NCR1, EOMES however also some expression of IL23R, RORC, AHR characteristic of ILC3, and GATA3 characteristic of ILC2. Had highest expression of SELL and ID2 in the ILCs which has been associated with more naive ILCs (see DOI)
Rationale DOI: https://doi.org/10.1038/ni.3368

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