An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

FDC

Ontology Term: follicular dendritic cellCL:0000442
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.: follicular dendritic cellCL:0000442
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLU, FDCSP, CXCL13, CR2
Canonical Marker Genes: CLU, FDCSP, CXCL13, CR2
Rationale: This cluster expresses canonical markers of follicular dendritic cells, such as FDCSP, CLU, CR2, and CXCL13. Version 2.0 will provide a more granular annotation of this compartment, including CD14+CD55+ FDC, COL27A1+ FDC, Fibroblastic Reticular Cells (FRC) and marginal reticular cells (MRC). Several of these clusters expressed multiple collagens, such as COL1A1, COL1A2, and COL6A3.
Rationale DOI: 10.1084/jem.20210790 10.1016/j.immuni.2018.04.006 10.1158/1078-0432.CCR-13-2367

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: follicular dendritic cellCL:0000442
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.: follicular dendritic cellCL:0000442
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CLU, FDCSP, CXCL13, CR2
Canonical Marker Genes: CLU, FDCSP, CXCL13, CR2
Rationale: This cluster expresses canonical markers of follicular dendritic cells, such as FDCSP, CLU, CR2, and CXCL13. Version 2.0 will provide a more granular annotation of this compartment, including CD14+CD55+ FDC, COL27A1+ FDC, Fibroblastic Reticular Cells (FRC) and marginal reticular cells (MRC). Several of these clusters expressed multiple collagens, such as COL1A1, COL1A2, and COL6A3.
Rationale DOI: 10.1084/jem.20210790 10.1016/j.immuni.2018.04.006 10.1158/1078-0432.CCR-13-2367

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