An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

preB/T

Full Name: precursor B/T cell
Closest Ontology Term: precursor B cellCL:0000817
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: pre-B cell
CategoryClass of which the cell type is a subclass.: precursor B cellCL:0000817
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: VPREB1, RAG1, RAG2, DNTT, CD1A, CD1B, CD1C, CD1E
Canonical Marker Genes: VPREB1, RAG1, RAG2, DNTT, CD1A, CD1B, CD1C, CD1E
Rationale: These cluster expressed members of the VDJ recombinase (RAG1, RAG2, DNTT), and markers of B and T cells. The expression of CD1A is consistent with a publication describing extrathymyc development of T cells in human tonsils.
Rationale DOI: 10.1172/JCI46125

Set of Labels Description: 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.
Annotation Method: manual

Full Name: precursor B/T cell
Closest Ontology Term: precursor B cellCL:0000817
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: pre-B cell
CategoryClass of which the cell type is a subclass.: precursor B cellCL:0000817
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: VPREB1, RAG1, RAG2, DNTT, CD1A, CD1B, CD1C, CD1E
Canonical Marker Genes: VPREB1, RAG1, RAG2, DNTT, CD1A, CD1B, CD1C, CD1E
Rationale: These cluster expressed members of the VDJ recombinase (RAG1, RAG2, DNTT), and markers of B and T cells. The expression of CD1A is consistent with a publication describing extrathymyc development of T cells in human tonsils.
Rationale DOI: 10.1172/JCI46125

Set of Labels Description: 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.
Annotation Method: manual