Marker Gene EvidenceGene 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).
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.