Cluster with high expression of CXCR4 (a marker defining DZ GCB cells) and additional expression of DZ markers, such as AICDA and MME, as well as moderate expression of AICDA. This cluster also has a clear expression of cell cycle genes, including MKI67, TOP2A, and PCLAF. (Bar-Joseph et al., 2008; Holmes et al., 2020; King et al., 2021; Milpied et al., 2018)
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.
