This relatively large cluster is characterized by rather intermediate or low expression of DZ markers, such as CXCR4. The cells start to express some LZ markers such as CD83 or LMO2, but still are missing other LZ-genes such as BCL2A1 or DUSP2. Furthermore, we could not define clear markers specific and unique for this cluster.
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.
