An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 Non-TFH

Full Name: CD4 Non-T follicular helper cell
Closest Ontology Term: helper T cellCL:0000912
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: T-helper cell, helper T-lymphocyte, helper T lymphocyte, helper T-cell, CD4 Non-Tfh
Category Class of which the cell type is a subclass.: T cellCL:0000084
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD3D, CD3E, CD3G, CD4
Canonical Marker Genes: CD3D, CD3E, CD3G, CD4
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). Non-Tfh cells represent a broad category -introduced in the review articles from Dr. Shane Crotty- that encompasses effector memory CD4 T cells, Th1, Th2, Th17 and Th22 cells. In version 2.0, we will provide all such categories, consistent with Figure 2 of our publication.
Rationale DOI: 10.1146/annurev-immunol-031210-101400 10.1016/j.immuni.2019.04.011 10.1002/eji.201343751

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

Full Name: CD4 Non-T follicular helper cell
Closest Ontology Term: helper T cellCL:0000912
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: T-helper cell, helper T-lymphocyte, helper T lymphocyte, helper T-cell, CD4 Non-Tfh
Category Class of which the cell type is a subclass.: T cellCL:0000084
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD3D, CD3E, CD3G, CD4
Canonical Marker Genes: CD3D, CD3E, CD3G, CD4
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). Non-Tfh cells represent a broad category -introduced in the review articles from Dr. Shane Crotty- that encompasses effector memory CD4 T cells, Th1, Th2, Th17 and Th22 cells. In version 2.0, we will provide all such categories, consistent with Figure 2 of our publication.
Rationale DOI: 10.1146/annurev-immunol-031210-101400 10.1016/j.immuni.2019.04.011 10.1002/eji.201343751

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