An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

DZ GCB

Ontology Term: centroblastCL:0009112
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centroblast, DZ GCB, DZ Germinal Center B cells
CategoryClass of which the cell type is a subclass.: germinal center B cellCL:0000844
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: SUGCT, AICDA, CXCR4, MME, CD38
Canonical Marker Genes: CXCR4, AICDA, MME
Rationale: Cluster with high expression of CXCR4 (a marker defining DZ GCB cells) and additional expression of DZ markers, such as FOXP1 and MME, as well as moderate expression of AICDA. Cells from these clusters are clearly non-proliferative, lacking the detectable expression of any cell cycle gene. Therefore, we hypothesize that cells in this cluster, although they maintain the expression of dark zone-related genes, have already finished the cell cycle program and are progressing towards the next maturation stage. (Bar-Joseph et al., 2008; Holmes et al., 2020; King et al., 2021; Milpied et al., 2018)
Rationale DOI: 10.1073/pnas.0704723105 10.1084/jem.20200483 10.1126/sciimmunol.abe6291 10.1038/s41590-018-0181-4

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: centroblastCL:0009112
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centroblast, DZ GCB, DZ Germinal Center B cells
CategoryClass of which the cell type is a subclass.: germinal center B cellCL:0000844
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: SUGCT, AICDA, CXCR4, MME, CD38
Canonical Marker Genes: CXCR4, AICDA, MME
Rationale: Cluster with high expression of CXCR4 (a marker defining DZ GCB cells) and additional expression of DZ markers, such as FOXP1 and MME, as well as moderate expression of AICDA. Cells from these clusters are clearly non-proliferative, lacking the detectable expression of any cell cycle gene. Therefore, we hypothesize that cells in this cluster, although they maintain the expression of dark zone-related genes, have already finished the cell cycle program and are progressing towards the next maturation stage. (Bar-Joseph et al., 2008; Holmes et al., 2020; King et al., 2021; Milpied et al., 2018)
Rationale DOI: 10.1073/pnas.0704723105 10.1084/jem.20200483 10.1126/sciimmunol.abe6291 10.1038/s41590-018-0181-4

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