An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

LZ GCB

Ontology Term: centrocyteCL:0009111
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centrocyte, Light Zone Germinal Center B cell
Category Class of which the cell type is a subclass.: germinal center B cellCL:0000844
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: In the literature one can found these cells as "LZ GCB" or "centrocytes". The community needs to come to an agreement on which term to use.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD83, LMO2, RGS13, MEF2B, BCL2A1
Canonical Marker Genes: CD83, LMO2, RGS13, BCL2A1
Rationale: Cells in this cluster show expression of well-known light zone markers, i.e. CD83, LMO2, and downregulation of DZ genes such as CXCR4 or AICDA. Within this cluster, genes related to CD40 signaling and response to BCR stimulation are starting to be expressed (e.g. BCL2A1, BCL2L1, TRAF1/4 or EBI3). However, the expression levels of these genes were not homogeneous, suggesting the presence of different levels of activation of LZ cells.
Rationale DOI: 10.1126/sciimmunol.abe6291 10.1016/j.it.2022.01.003 10.1016/j.immuni.2020.06.013

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: centrocyteCL:0009111
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centrocyte, Light Zone Germinal Center B cell
Category Class of which the cell type is a subclass.: germinal center B cellCL:0000844
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: In the literature one can found these cells as "LZ GCB" or "centrocytes". The community needs to come to an agreement on which term to use.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD83, LMO2, RGS13, MEF2B, BCL2A1
Canonical Marker Genes: CD83, LMO2, RGS13, BCL2A1
Rationale: Cells in this cluster show expression of well-known light zone markers, i.e. CD83, LMO2, and downregulation of DZ genes such as CXCR4 or AICDA. Within this cluster, genes related to CD40 signaling and response to BCR stimulation are starting to be expressed (e.g. BCL2A1, BCL2L1, TRAF1/4 or EBI3). However, the expression levels of these genes were not homogeneous, suggesting the presence of different levels of activation of LZ cells.
Rationale DOI: 10.1126/sciimmunol.abe6291 10.1016/j.it.2022.01.003 10.1016/j.immuni.2020.06.013

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