An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

CD8 TCM

Full Name: CD8 central memory T cell
Closest Ontology Term: CD4-positive, alpha-beta memory T cell, CD45RO-positiveCL:0001204
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: CD4-positive, alpha-beta memory T-cell, CD45RO-positive, CD4-positive, alpha-beta memory T lymphocyte, CD45RO-positive, CD4-positive, alpha-beta memory T-lymphocyte, CD45RO-positive
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, CD8A, CD8B, IL7R, ANXA1, S100A4
Canonical Marker Genes: CD3D, CD3E, CD8A, CD8B, IL7R, ANXA1, S100A4
Rationale: CM CD8 T cells acquire memory (marked by IL7R+) while maintaining lymph node homing capacity (CCR7+). CM CD8 T cells expressed higher levels of IL7R compared to naïve T cells, and higher expression of ANXA1 and S100A4. They had an intermediate expression of CCR7 and a higher expression of CD28. At the protein level, this cluster was CD45RO+, and CD28+. This cluster has a very similar gene expression profile to CD4 TCM. While CD4 transcripts are usually not detected in scRNA-seq data, both CD8A and CD8B are detectable and used to differentiate both cell types.
Rationale DOI: 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: CD8 central memory T cell
Closest Ontology Term: CD4-positive, alpha-beta memory T cell, CD45RO-positiveCL:0001204
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: CD4-positive, alpha-beta memory T-cell, CD45RO-positive, CD4-positive, alpha-beta memory T lymphocyte, CD45RO-positive, CD4-positive, alpha-beta memory T-lymphocyte, CD45RO-positive
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, CD8A, CD8B, IL7R, ANXA1, S100A4
Canonical Marker Genes: CD3D, CD3E, CD8A, CD8B, IL7R, ANXA1, S100A4
Rationale: CM CD8 T cells acquire memory (marked by IL7R+) while maintaining lymph node homing capacity (CCR7+). CM CD8 T cells expressed higher levels of IL7R compared to naïve T cells, and higher expression of ANXA1 and S100A4. They had an intermediate expression of CCR7 and a higher expression of CD28. At the protein level, this cluster was CD45RO+, and CD28+. This cluster has a very similar gene expression profile to CD4 TCM. While CD4 transcripts are usually not detected in scRNA-seq data, both CD8A and CD8B are detectable and used to differentiate both cell types.
Rationale DOI: 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