An Atlas of Cells in the Human Tonsil

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Summary

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Cell Metadata

cell_type_azimuth

Epithelial

Full Name: tonsil epithelial cell
Closest Ontology Term: tonsil squamous cellCL:1001577
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: tonsil squamous epithelial cells, tonsillar squamous cell, tonsil squamous epithelial cell, tonsillar squamous epithelial cell, tonsillar epithelial cell
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cells in one of the epithelial clusters expressed SPIB and MARCKSL1, two genes associated with microfold cells (M cells), which are responsible for the uptake of antigens in the tonsillar lumen (Kobayashi et al., 2019).
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: KRT19, KRT13, KRT18, KRT14, KRT5, LCE3D, SPINK5, SPRR3, SPRR1B
Canonical Marker Genes: KRT19, KRT13, KRT18, KRT14, KRT5, LCE3D, SPINK5, SPRR3, SPRR1B
Rationale: This cluster represents the epithelial cells of the tonsil, characterized by the expression of several cytokeratins (e.g. KRT5, KRT19). In version 2.0, we will further stratify it into basal, surface, outer surface and crypt layers. One of these clusters expressed FDCSP (FDCSP epithelium). FDCSP was first described in FDC and in ‘‘leukocyte-infiltrated tonsillar crypts,’’ although the specific population within the crypts remained unknown. We provide evidence that FDSCP-expressing cells represent a specific subpopulation of the tonsillar epithelium, in line with a cluster observed in the oral mucosa cell atlas.
Rationale DOI: 10.1016/j.cell.2021.05.013 10.1084/jem.20210790 10.3389/fimmu.2019.02345

Inherited from cell_type_azimuth

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

Epithelial

Full Name: tonsil epithelial cell
Closest Ontology Term: tonsil squamous cellCL:1001577
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: tonsil squamous epithelial cells, tonsillar squamous cell, tonsil squamous epithelial cell, tonsillar squamous epithelial cell, tonsillar epithelial cell
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: Cells in one of the epithelial clusters expressed SPIB and MARCKSL1, two genes associated with microfold cells (M cells), which are responsible for the uptake of antigens in the tonsillar lumen (Kobayashi et al., 2019).
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: KRT19, KRT13, KRT18, KRT14, KRT5, LCE3D, SPINK5, SPRR3, SPRR1B
Canonical Marker Genes: KRT19, KRT13, KRT18, KRT14, KRT5, LCE3D, SPINK5, SPRR3, SPRR1B
Rationale: This cluster represents the epithelial cells of the tonsil, characterized by the expression of several cytokeratins (e.g. KRT5, KRT19). In version 2.0, we will further stratify it into basal, surface, outer surface and crypt layers. One of these clusters expressed FDCSP (FDCSP epithelium). FDCSP was first described in FDC and in ‘‘leukocyte-infiltrated tonsillar crypts,’’ although the specific population within the crypts remained unknown. We provide evidence that FDSCP-expressing cells represent a specific subpopulation of the tonsillar epithelium, in line with a cluster observed in the oral mucosa cell atlas.
Rationale DOI: 10.1016/j.cell.2021.05.013 10.1084/jem.20210790 10.3389/fimmu.2019.02345

Inherited from cell_type_azimuth

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