An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

PC

Ontology Term: plasma cellCL:0000786
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: plasma B cell, plasmocyte, plasma B-cell, plasmacyte
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: XBP1, IRF4, PRDM1, DERL3, FKBP11, MZB1
Canonical Marker Genes: XBP1, IRF4, PRDM1, DERL3, FKBP11, MZB1
Rationale: This cluster corresponds to fully-differentiated plasma cells. These cells express high levels of the 3 bona-fide PC transcription factors (XBP1, IRF4, PRDM1), as well as PC phenotypic markers (MZB1, DERL3). They do not express any cell cycle gene.
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: plasma cellCL:0000786
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: plasma B cell, plasmocyte, plasma B-cell, plasmacyte
CategoryClass of which the cell type is a subclass.: plasma cellCL:0000786
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: XBP1, IRF4, PRDM1, DERL3, FKBP11, MZB1
Canonical Marker Genes: XBP1, IRF4, PRDM1, DERL3, FKBP11, MZB1
Rationale: This cluster corresponds to fully-differentiated plasma cells. These cells express high levels of the 3 bona-fide PC transcription factors (XBP1, IRF4, PRDM1), as well as PC phenotypic markers (MZB1, DERL3). They do not express any cell cycle gene.
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