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.
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.
