An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

DC

Ontology Term: dendritic cellCL:0000451
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
CategoryClass of which the cell type is a subclass.: dendritic cellCL:0000451
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LYZ, CST3, LGALS3, FCER1A, CLEC9A, SIGLEC10
Canonical Marker Genes: LYZ, CST3, LGALS3, FCER1A, CLEC9A, SIGLEC10
Rationale: The dendritic cell subsets described in the tonsil atlas overlap with the ones provided by Villani, et al. (2017) in peripheral blood: DC1, conventional DC1 (cDC1, e.g. CLEC9A), divided into precursor and mature states on the basis of XCR1 expression (Balan et al., 2018); (2) DC2 and DC3, corresponding to cDC2 (CD1C, FCER1A, CLEC10A) and differing in their antigen-presenting capacity (e.g. HLA-DQB1) and inflammatory signatures (S100A8, S100A9), respectively; (3) DC4 (FCGR3A, SERPINA1 and FTL) putatively derive from non-classical monocytes; and (4) DC5 expressing AXL and SIGLEC6 (AS), the hallmark markers of AS DCs These subsets will be available in version 2.0.
Rationale DOI: 10.1126/science.aah4573 10.1016/j.celrep.2018.07.033

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.: unknown
CategoryClass of which the cell type is a subclass.: dendritic cellCL:0000451
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: LYZ, CST3, LGALS3, FCER1A, CLEC9A, SIGLEC10
Canonical Marker Genes: LYZ, CST3, LGALS3, FCER1A, CLEC9A, SIGLEC10
Rationale: The dendritic cell subsets described in the tonsil atlas overlap with the ones provided by Villani, et al. (2017) in peripheral blood: DC1, conventional DC1 (cDC1, e.g. CLEC9A), divided into precursor and mature states on the basis of XCR1 expression (Balan et al., 2018); (2) DC2 and DC3, corresponding to cDC2 (CD1C, FCER1A, CLEC10A) and differing in their antigen-presenting capacity (e.g. HLA-DQB1) and inflammatory signatures (S100A8, S100A9), respectively; (3) DC4 (FCGR3A, SERPINA1 and FTL) putatively derive from non-classical monocytes; and (4) DC5 expressing AXL and SIGLEC6 (AS), the hallmark markers of AS DCs These subsets will be available in version 2.0.
Rationale DOI: 10.1126/science.aah4573 10.1016/j.celrep.2018.07.033

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