An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 TCM

Full Name: CD4 central memory T cell
Closest Ontology Term: memory T cellCL:0000813
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: memory T lymphocyte, memory T-lymphocyte, memory T-cell, CM CD4 T cell
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, CD3G, IL7R, TCF7, ANXA1, ANK3, PASK, S100A4
Canonical Marker Genes: CD3D, CD3G, IL7R, TCF7, ANXA1, PASK, S100A4
Rationale: After antigen encounter T cells acquire memory and effector functions maintaining the lymph node homing. CM showed an upregulation of IL7R compared to naïve T cells, and higher expression of PRDM1, PASK, ANXA1 and S100A4. They had an intermediate expression of CCR7 and higher expression of CD28 confirming their migratory capacity to secondary lymph nodes and their memory profile based on their effector function. This cluster expressed CD45RO at the protein level.
Rationale DOI: 10.1038/s41467-020-15543-y 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 central memory T cell
Closest Ontology Term: memory T cellCL:0000813
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: memory T lymphocyte, memory T-lymphocyte, memory T-cell, CM CD4 T cell
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, CD3G, IL7R, TCF7, ANXA1, ANK3, PASK, S100A4
Canonical Marker Genes: CD3D, CD3G, IL7R, TCF7, ANXA1, PASK, S100A4
Rationale: After antigen encounter T cells acquire memory and effector functions maintaining the lymph node homing. CM showed an upregulation of IL7R compared to naïve T cells, and higher expression of PRDM1, PASK, ANXA1 and S100A4. They had an intermediate expression of CCR7 and higher expression of CD28 confirming their migratory capacity to secondary lymph nodes and their memory profile based on their effector function. This cluster expressed CD45RO at the protein level.
Rationale DOI: 10.1038/s41467-020-15543-y 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