An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

PDC

Ontology Term: plasmacytoid dendritic cellCL:0000784
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: IPC, pDC, type 2 DC
Category Class of which the cell type is a subclass.: plasmacytoid dendritic cellCL:0000784
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LILRA4, IL3RA, IRF8, CST3
Canonical Marker Genes: LILRA4, IL3RA, IRF8, CST3
Rationale: pDCs were previously identified by the standard protein marker CD123 (IL3RA). This cluster had higher expression of IRF8, IL3RA and LILRA4. One subcluster additionally expressed interferon-related genes (IFI44, IFI6).
Rationale DOI: 10.1038/s41467-018-05784-3

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: plasmacytoid dendritic cellCL:0000784
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: IPC, pDC, type 2 DC
Category Class of which the cell type is a subclass.: plasmacytoid dendritic cellCL:0000784
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: LILRA4, IL3RA, IRF8, CST3
Canonical Marker Genes: LILRA4, IL3RA, IRF8, CST3
Rationale: pDCs were previously identified by the standard protein marker CD123 (IL3RA). This cluster had higher expression of IRF8, IL3RA and LILRA4. One subcluster additionally expressed interferon-related genes (IFI44, IFI6).
Rationale DOI: 10.1038/s41467-018-05784-3

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