An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 TFH Mem

Ontology Term: T follicular helper cellCL:0002038
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T(FH) memory, follicular helper memory T cell, Tfh memory
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, KLRB1, MAF, TOX2, ICOS, IL21
Canonical Marker Genes: CD3D, CD3E, KLRB1, MAF, TOX2, ICOS, IL21, CD4
Rationale: Upon leaving a GC, the Tfh cell acquires a less activated, less polarized Tfh phenotype and can upregulate KLRB1 and develop into resting memory Tfh cells. This cluster had the expression of follicular markers PDCD1, MAF, and higher expression of memory markers such as KLRB1, ITGB1, and CD28
Rationale DOI: 10.1016/j.immuni.2014.10.004 10.4049/jimmunol.1002828 10.1016/j.immuni.2013.08.031 10.1002/eji.201242540

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) memory, follicular helper memory T cell, Tfh memory
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, KLRB1, MAF, TOX2, ICOS, IL21
Canonical Marker Genes: CD3D, CD3E, KLRB1, MAF, TOX2, ICOS, IL21, CD4
Rationale: Upon leaving a GC, the Tfh cell acquires a less activated, less polarized Tfh phenotype and can upregulate KLRB1 and develop into resting memory Tfh cells. This cluster had the expression of follicular markers PDCD1, MAF, and higher expression of memory markers such as KLRB1, ITGB1, and CD28
Rationale DOI: 10.1016/j.immuni.2014.10.004 10.4049/jimmunol.1002828 10.1016/j.immuni.2013.08.031 10.1002/eji.201242540

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