An Atlas of Cells in the Human Tonsil

Tonsils are constantly exposed to antigens through the upper respiratory tract, making them a valuable secondary lymphoid organ (SLO) for studying the interaction between innate and adaptive immune cells during germinal center (GC) development, which is crucial for building adaptive immunity. This reference includes 377,963 cells (10x Genomics 3' v3) from 17 healthy human donors spanning various age groups, including children, young adults, and older adults.

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.

The tonsil atlas is a FAIR resource—findable, accessible, interoperable, and reusable. The raw data has been deposited in ArrayExpress and can be remapped and reanalyzed by following the instructions provided in the TonsilAtlas and TonsilAtlasCAP GitHub repositories. The resulting expression matrices and Seurat objects are available on Zenodo, and the data can be accessed, explored, interpreted, and reused via the HCATonsilAtlas Bioconductor package and the Azimuth web interface. Additionally, we provide a detailed glossary of the marker genes, rationales, and publications used to annotate each cell type and state. The external URLs section contains links to all these resources.