An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

ILC

Ontology Term: innate lymphoid cellCL:0001065
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: ILC, CD127+ ILC
CategoryClass of which the cell type is a subclass.: innate lymphoid cellCL:0001065
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: IL7R, FCER1G, GNLY, CD200R1, RORC, IL23R
Canonical Marker Genes: IL7R, FCER1G, GNLY, CD200R1, RORC, IL23R
Rationale: This cluster contains ILC1, NKp44+ ILC3 and NKp44- ILC3. ILC1 are characterized by their capacity to produce IFNγ and they depend on the transcription factor T-bet. Contrary to NK cells, ILC1 express IL7R (CD127) and CD200R; and do not express KLRF1 (NKp80). Accordingly, this cluster expressed high levels of IL7R, CD200R1, CD69 and ANXA1; and did not express KLRF1 (Boldt et al., 2014; Vivier et al., 2018) ILC3s depend on RORC for their development and function, and comprise subsets that can be distinguished on the basis of expression of the natural cytotoxicity receptors NKp46 and NKp44. The main cytokine produced by ILC3s is IL-22 and a proportion of ILC3s also produce IL-17. We identified two subtypes of ILC3s that expressed RORC and IL23R; and were NKp44 (NCR2) positive and negative (Bal et al., 2020; Vivier et al., 2018) This -more granular- classification will be provided in version 2.0, in line with our paper
Rationale DOI: 10.1002/cyto.b.21162 10.1016/j.cell.2018.07.017 10.1038/s41577-020-0282-9

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: innate lymphoid cellCL:0001065
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: ILC, CD127+ ILC
CategoryClass of which the cell type is a subclass.: innate lymphoid cellCL:0001065
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: IL7R, FCER1G, GNLY, CD200R1, RORC, IL23R
Canonical Marker Genes: IL7R, FCER1G, GNLY, CD200R1, RORC, IL23R
Rationale: This cluster contains ILC1, NKp44+ ILC3 and NKp44- ILC3. ILC1 are characterized by their capacity to produce IFNγ and they depend on the transcription factor T-bet. Contrary to NK cells, ILC1 express IL7R (CD127) and CD200R; and do not express KLRF1 (NKp80). Accordingly, this cluster expressed high levels of IL7R, CD200R1, CD69 and ANXA1; and did not express KLRF1 (Boldt et al., 2014; Vivier et al., 2018) ILC3s depend on RORC for their development and function, and comprise subsets that can be distinguished on the basis of expression of the natural cytotoxicity receptors NKp46 and NKp44. The main cytokine produced by ILC3s is IL-22 and a proportion of ILC3s also produce IL-17. We identified two subtypes of ILC3s that expressed RORC and IL23R; and were NKp44 (NCR2) positive and negative (Bal et al., 2020; Vivier et al., 2018) This -more granular- classification will be provided in version 2.0, in line with our paper
Rationale DOI: 10.1002/cyto.b.21162 10.1016/j.cell.2018.07.017 10.1038/s41577-020-0282-9

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