An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

prePB

Full Name: precursor plasmablast
Closest Ontology Term: plasmablastCL:0000980
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: precursor PB
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: RGS13, MEF2B, PAX5, MS4A1, XBP1, VDR, PRDM1
Canonical Marker Genes: RGS13, MEF2B, PAX5, MS4A1, XBP1, VDR, PRDM1
Rationale: This cluster still has phenotypic markers of LZ GCBC (centrocytes, such as RGS13, MEF2B), as well as pan-B cell markers (PAX5, MS4A1). However, it already expresses PC-specific markers, such as XBP1, VDR and PRDM1.
Rationale DOI: 10.1038/nri3795 10.1126/sciimmunol.abe6291

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 plasmablast
Closest Ontology Term: plasmablastCL:0000980
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: precursor PB
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: RGS13, MEF2B, PAX5, MS4A1, XBP1, VDR, PRDM1
Canonical Marker Genes: RGS13, MEF2B, PAX5, MS4A1, XBP1, VDR, PRDM1
Rationale: This cluster still has phenotypic markers of LZ GCBC (centrocytes, such as RGS13, MEF2B), as well as pan-B cell markers (PAX5, MS4A1). However, it already expresses PC-specific markers, such as XBP1, VDR and PRDM1.
Rationale DOI: 10.1038/nri3795 10.1126/sciimmunol.abe6291

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