An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD4 TREG

Ontology Term: regulatory T cellCL:0000815
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: regulatory T-lymphocyte, regulatory T-cell, regulatory T lymphocyte, suppressor T cell, suppressor T lymphocyte, suppressor T-lymphocyte, Treg, suppressor T-cell, regulatory 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, CD3E, CD2, CYTOR, IL10, FOXP3, CTLA4, IL2RA
Canonical Marker Genes: CD3D, CD3E, CD2, CD4, IL10, FOXP3, CTLA4, IL2RA
Rationale: CD4 T regulatory (Treg) cells are vital for the maintenance of immune tolerance, and are characterized by the expression of cytokine IL10, the transcription factor FOXP3 and the expression of IL2RA (CD25) and CTLA4. In version 2.0, we will further subdivide this cluster into effector Tregs and T follicular regulatory cells.
Rationale DOI: 10.1007/978-981-15-6407-9_1 10.1073/pnas.1705551114

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: regulatory T cellCL:0000815
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: regulatory T-lymphocyte, regulatory T-cell, regulatory T lymphocyte, suppressor T cell, suppressor T lymphocyte, suppressor T-lymphocyte, Treg, suppressor T-cell, regulatory 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, CD3E, CD2, CYTOR, IL10, FOXP3, CTLA4, IL2RA
Canonical Marker Genes: CD3D, CD3E, CD2, CD4, IL10, FOXP3, CTLA4, IL2RA
Rationale: CD4 T regulatory (Treg) cells are vital for the maintenance of immune tolerance, and are characterized by the expression of cytokine IL10, the transcription factor FOXP3 and the expression of IL2RA (CD25) and CTLA4. In version 2.0, we will further subdivide this cluster into effector Tregs and T follicular regulatory cells.
Rationale DOI: 10.1007/978-981-15-6407-9_1 10.1073/pnas.1705551114

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