An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

preMBC/doublet

Full Name: precursor memory B cell
Closest Ontology Term: memory B cellCL:0000787
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
CategoryClass of which the cell type is a subclass.: memory B cellCL:0000787
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CCR6, MEF2B, CD22, CELF2
Canonical Marker Genes: CCR6, MEF2B, CD22, CELF2
Rationale: This cluster was characterized by high expression of CCR6 or CELF2, genes that are commonly used in literature to define memory B cell precursors (Holmes et al., 2020). Although this cluster likely represents early MBCs derived from the LZ, we cannot exclude some technical issues or even MBC-GC doublet cells.
Rationale DOI: 10.1084/jem.20200483

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

Full Name: precursor memory B cell
Closest Ontology Term: memory B cellCL:0000787
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
CategoryClass of which the cell type is a subclass.: memory B cellCL:0000787
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CCR6, MEF2B, CD22, CELF2
Canonical Marker Genes: CCR6, MEF2B, CD22, CELF2
Rationale: This cluster was characterized by high expression of CCR6 or CELF2, genes that are commonly used in literature to define memory B cell precursors (Holmes et al., 2020). Although this cluster likely represents early MBCs derived from the LZ, we cannot exclude some technical issues or even MBC-GC doublet cells.
Rationale DOI: 10.1084/jem.20200483

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