An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

preGCB

Ontology Term: tonsil germinal center B cellCL:2000006
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: preGCB, precursor tonsil germinal center B cell
CategoryClass of which the cell type is a subclass.: B cellCL:0000236
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: BATF, MEF2B, RGS13, BCL2A1, TCL1A, LMO2, NME2, NPM1, FCER2
Canonical Marker Genes: BATF, MEF2B, RGS13, BCL2A1, TCL1A, LMO2, NME2, NPM1, FCER2
Rationale: Cells in this cluster express typical NBC markers such as FCER2 (CD23) and. As compared to "B activated cells", within this cluster we could detect the expression of GC-specific genes, such as RGS13, MEF2B, LMO2. (King et al., 2021). However, these cells still partially maintain the NBC transcriptome and transcriptional programs started in the previous steps of NBC activation process (i.e. GC-committed NBC) such as the BATF expression and MYC targets (NPM1, NME2). Additionally, this cluster still lacks other GC phenotypic genes, such as AICDA or BCL6. Therefore, we conclude that this subcluster may represent the last step of NBC activation before entering into the DZ and starting a proper GC reaction.
Rationale DOI: 10.1126/sciimmunol.abe6291

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

Ontology Term: tonsil germinal center B cellCL:2000006
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: preGCB, precursor tonsil germinal center B cell
CategoryClass of which the cell type is a subclass.: B cellCL:0000236
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: BATF, MEF2B, RGS13, BCL2A1, TCL1A, LMO2, NME2, NPM1, FCER2
Canonical Marker Genes: BATF, MEF2B, RGS13, BCL2A1, TCL1A, LMO2, NME2, NPM1, FCER2
Rationale: Cells in this cluster express typical NBC markers such as FCER2 (CD23) and. As compared to "B activated cells", within this cluster we could detect the expression of GC-specific genes, such as RGS13, MEF2B, LMO2. (King et al., 2021). However, these cells still partially maintain the NBC transcriptome and transcriptional programs started in the previous steps of NBC activation process (i.e. GC-committed NBC) such as the BATF expression and MYC targets (NPM1, NME2). Additionally, this cluster still lacks other GC phenotypic genes, such as AICDA or BCL6. Therefore, we conclude that this subcluster may represent the last step of NBC activation before entering into the DZ and starting a proper GC reaction.
Rationale DOI: 10.1126/sciimmunol.abe6291

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