An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

Mono/Macro

Full Name: Monocytes/Macrophages
Closest Ontology Term: macrophageCL:0000235
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: macrophageCL:0000235
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LYZ, CST3, CD68, S100A8, S100A9
Canonical Marker Genes: LYZ, CST3, CD68, S100A8, S100A9
Rationale: This cluster expresses markers of monocytes and macrophages. Surprisingly, these cells also expressed markers specific of tonsillar slan+ cells. We identified several slan-like clusters, which we will provide in version 2.0.
Rationale DOI: 10.1096/fj.202000181R

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: Monocytes/Macrophages
Closest Ontology Term: macrophageCL:0000235
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: macrophageCL:0000235
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LYZ, CST3, CD68, S100A8, S100A9
Canonical Marker Genes: LYZ, CST3, CD68, S100A8, S100A9
Rationale: This cluster expresses markers of monocytes and macrophages. Surprisingly, these cells also expressed markers specific of tonsillar slan+ cells. We identified several slan-like clusters, which we will provide in version 2.0.
Rationale DOI: 10.1096/fj.202000181R

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