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

Main

Cell Metadata

Stromal_cells

Ontology Term: stromal cellCL:0000499
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.: connective tissue cellCL:0002320
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CO1A2, COL3A1, CCL19, CXCL14, CLU, SOX5
Canonical Marker Genes: CO1A2, COL3A1, CCL19,
Rationale: Relative lack of PTPRC compared to other subsets, expression of collagens, SOX5 and PDPN (gp38)
Rationale DOI: https://doi.org/10.1038/s41556-022-00866-3; DOI: 10.1084/jem.20210790

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

Main

Cell Metadata

Ontology Term: stromal cellCL:0000499
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.: connective tissue cellCL:0002320
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CO1A2, COL3A1, CCL19, CXCL14, CLU, SOX5
Canonical Marker Genes: CO1A2, COL3A1, CCL19,
Rationale: Relative lack of PTPRC compared to other subsets, expression of collagens, SOX5 and PDPN (gp38)
Rationale DOI: https://doi.org/10.1038/s41556-022-00866-3; DOI: 10.1084/jem.20210790

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