After antigen recognition in the T cell zone, CD4 T cells can either differentiate into non-T follicular helper (non-Tfh, regulated by PRDM1) or Tfh (regulated by BCL6). Non-Tfh cells represent a broad category -introduced in the review articles from Dr. Shane Crotty- that encompasses effector memory CD4 T cells, Th1, Th2, Th17 and Th22 cells. In version 2.0, we will provide all such categories, consistent with Figure 2 of our publication.
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.
