An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

B memory

Ontology Term: memory B cellCL:0000787
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: memory B-cell, memory B-lymphocyte, memory B lymphocyte
Category Class of which the cell type is a subclass.: B cellCL:0000236
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD27, BANK1, MARCH1, TNFRSF13B, BLK, CD24
Canonical Marker Genes: CD19, CD27, TNFRSF13B, CD24
Rationale: Memory B cells are a vital subset of the adaptive immune system, distinguished by their long-lived nature and ability to persist for decades after initial antigen exposure. These cells circulate in a quiescent state and rapidly respond to re-exposure to their specific antigen, quickly differentiating into antibody-producing plasma cells, thereby ensuring a faster and more robust secondary immune response compared to naive B cells. They retain antigen specificity and can express various immunoglobulin isotypes, often originating from germinal centers in secondary lymphoid organs. Memory B cells are essential for long-term immunity and the effectiveness of vaccines. They can be further stratified into class-switched (IgG+ or IgA+) or non-class switch (IgD or IgM), and they differ from naive B cells by the expression of CD27 and negativity for TCL1A and FCER2
Rationale DOI: 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: memory B cellCL:0000787
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: memory B-cell, memory B-lymphocyte, memory B lymphocyte
Category Class of which the cell type is a subclass.: B cellCL:0000236
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD27, BANK1, MARCH1, TNFRSF13B, BLK, CD24
Canonical Marker Genes: CD19, CD27, TNFRSF13B, CD24
Rationale: Memory B cells are a vital subset of the adaptive immune system, distinguished by their long-lived nature and ability to persist for decades after initial antigen exposure. These cells circulate in a quiescent state and rapidly respond to re-exposure to their specific antigen, quickly differentiating into antibody-producing plasma cells, thereby ensuring a faster and more robust secondary immune response compared to naive B cells. They retain antigen specificity and can express various immunoglobulin isotypes, often originating from germinal centers in secondary lymphoid organs. Memory B cells are essential for long-term immunity and the effectiveness of vaccines. They can be further stratified into class-switched (IgG+ or IgA+) or non-class switch (IgD or IgM), and they differ from naive B cells by the expression of CD27 and negativity for TCL1A and FCER2
Rationale DOI: 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