An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

PB

Ontology Term: plasmablastCL:0000980
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD27-positive, CD38-positive, CD20-negative B cell, CD20-negative B cell
CategoryClass of which the cell type is a subclass.: plasmablastCL:0000980
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: XBP1, MZB1, DERL3, CENPA, PCLAF, JCHAIN, TOP2A
Canonical Marker Genes: XBP1, MZB1, TOP2A, DERL3
Rationale: Cells within this cluster are clearly proliferative plasmablasts with high expression levels of proliferation-related genes (H2AFZ, TUBA1B, MKI67 and TOP2A, among others). Otherwise have an expression pattern of PCs (the 3 transcription factors PRDM1, IRF4 and XBP1, as well as phenotypic markers MZB1, SLAMF7, SSR4, CREB3L2 and FKBP11).
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

Ontology Term: plasmablastCL:0000980
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: CD27-positive, CD38-positive, CD20-negative B cell, CD20-negative B cell
CategoryClass of which the cell type is a subclass.: plasmablastCL:0000980
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: XBP1, MZB1, DERL3, CENPA, PCLAF, JCHAIN, TOP2A
Canonical Marker Genes: XBP1, MZB1, TOP2A, DERL3
Rationale: Cells within this cluster are clearly proliferative plasmablasts with high expression levels of proliferation-related genes (H2AFZ, TUBA1B, MKI67 and TOP2A, among others). Otherwise have an expression pattern of PCs (the 3 transcription factors PRDM1, IRF4 and XBP1, as well as phenotypic markers MZB1, SLAMF7, SSR4, CREB3L2 and FKBP11).
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