An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

aDC

Ontology Term: dendritic cellCL:0000451
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: mregDCs, CCR7+ DC, migratory dendritic cell
CategoryClass of which the cell type is a subclass.: dendritic cellCL:0000451
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LAMP3, CCR7, PRDM16, CCL19, TREML1, CCL22
Canonical Marker Genes: LAMP3, CCR7, PRDM16, CCL19, TREML1, CCL22
Rationale: The hallmark of activated DC (aDC) is the high expression of CCR7, the chemokine needed to migrate to the T cell zone (that's why they are commonly referred to as migratory DC). They can produce cytokines that attract other CCR7-expressing cells to the T cell zone (such as CCL19). We could define 3 subsets of aDC in line with the thymus atlas, which will become available in version 2.0. These subsets, however, require validation.
Rationale DOI: 10.1126/science.aay3224 10.1002/ctm2.1199 10.1126/sciimmunol.abl5053

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: dendritic cellCL:0000451
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: mregDCs, CCR7+ DC, migratory dendritic cell
CategoryClass of which the cell type is a subclass.: dendritic cellCL:0000451
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LAMP3, CCR7, PRDM16, CCL19, TREML1, CCL22
Canonical Marker Genes: LAMP3, CCR7, PRDM16, CCL19, TREML1, CCL22
Rationale: The hallmark of activated DC (aDC) is the high expression of CCR7, the chemokine needed to migrate to the T cell zone (that's why they are commonly referred to as migratory DC). They can produce cytokines that attract other CCR7-expressing cells to the T cell zone (such as CCL19). We could define 3 subsets of aDC in line with the thymus atlas, which will become available in version 2.0. These subsets, however, require validation.
Rationale DOI: 10.1126/science.aay3224 10.1002/ctm2.1199 10.1126/sciimmunol.abl5053

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