An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 TFH

Ontology Term: T follicular helper cellCL:0002038
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T(FH), follicular helper T cell, follicular T-helper cell, follicular T-cell, follicular T cell, follicular B helper T cell, follicular helper T-cell, Tfh
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3D, CD3E, CD2, TIGIT, IL6ST, PDCD1, TOX2, ICOS, CXCR5, CXCL13
Canonical Marker Genes: CD3D, CD3E, CD2, TIGIT, IL6ST, PDCD1, TOX2, ICOS, CXCR5, CXCL13
Rationale: After antigen recognition in the T cell zone, CD4 T cells can either differentiate into non-T follicular helper (non-Tfh, regulated by PRDM1) or Tfh (regulated by BCL6). Tfh cells migrate to the follicles by upregulating CXCR5 (which binds to CXCL13) and downregulting CCR7. Tfh cells select centrocytes (LZ B cells) that have the highest affinity towards the antigen during the germinal center reaction. Their canonical markers are CXCR5, CXCL13, ICOS, PDCD1 and IL21.
Rationale DOI: 10.1016/j.it.2021.02.002 10.1146/annurev-immunol-031210-101400 10.1016/j.immuni.2019.04.011 10.1016/j.immuni.2014.10.004

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: T follicular helper cellCL:0002038
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T(FH), follicular helper T cell, follicular T-helper cell, follicular T-cell, follicular T cell, follicular B helper T cell, follicular helper T-cell, Tfh
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3D, CD3E, CD2, TIGIT, IL6ST, PDCD1, TOX2, ICOS, CXCR5, CXCL13
Canonical Marker Genes: CD3D, CD3E, CD2, TIGIT, IL6ST, PDCD1, TOX2, ICOS, CXCR5, CXCL13
Rationale: After antigen recognition in the T cell zone, CD4 T cells can either differentiate into non-T follicular helper (non-Tfh, regulated by PRDM1) or Tfh (regulated by BCL6). Tfh cells migrate to the follicles by upregulating CXCR5 (which binds to CXCL13) and downregulting CCR7. Tfh cells select centrocytes (LZ B cells) that have the highest affinity towards the antigen during the germinal center reaction. Their canonical markers are CXCR5, CXCL13, ICOS, PDCD1 and IL21.
Rationale DOI: 10.1016/j.it.2021.02.002 10.1146/annurev-immunol-031210-101400 10.1016/j.immuni.2019.04.011 10.1016/j.immuni.2014.10.004

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