An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

MBC-derived PC / doublets

Ontology Term: plasma cellCL:0000786
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: MBC-derived PC
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PRDM1, XBP1, FCMR, CCDC50
Canonical Marker Genes: PRDM1, XBP1, FCMR, CCDC50
Rationale: This cluster expresses both markers of markers of memory B cells (FCMR, CCDC50) and plasma cells (PRDM1, XBP1). Thus, it could represent a cluster of reactivated MBC that differentiated into PC. However, this population had a low annotation confidence in the validation cohort. Because it is composed of markers of two different cell types, we cannot rule out that they correspond to doublets.
Rationale DOI: 10.1038/nri3795

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: plasma cellCL:0000786
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: MBC-derived PC
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: PRDM1, XBP1, FCMR, CCDC50
Canonical Marker Genes: PRDM1, XBP1, FCMR, CCDC50
Rationale: This cluster expresses both markers of markers of memory B cells (FCMR, CCDC50) and plasma cells (PRDM1, XBP1). Thus, it could represent a cluster of reactivated MBC that differentiated into PC. However, this population had a low annotation confidence in the validation cohort. Because it is composed of markers of two different cell types, we cannot rule out that they correspond to doublets.
Rationale DOI: 10.1038/nri3795

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