An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

B naive

Ontology Term: naive B cellCL:0000788
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: naive B-cell, naive B-lymphocyte, naive B lymphocyte
CategoryClass of which the cell type is a subclass.: B cellCL:0000236
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: FCER2, TCL1A, IGHM, IGHD, MS4A1, CD79A
Canonical Marker Genes: FCER2, TCL1A, IGHM, MS4A1, CD79A
Rationale: The "B Naive” annotation represents the main cluster of naive (antigen-inexperienced) B cells, characterized by a clear and homogeneous expression of key markers including FCER2 (CD23), TCLA1, IGHM, and IGHD. In the “Cell types level 3 20230508” annotation set, this cluster will be further refined and subclustered into 8 distinct subpopulations.
Rationale DOI: 10.1016/j.it.2022.01.003 10.1016/j.immuni.2020.06.013

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: naive B cellCL:0000788
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: naive B-cell, naive B-lymphocyte, naive B lymphocyte
CategoryClass of which the cell type is a subclass.: B cellCL:0000236
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: FCER2, TCL1A, IGHM, IGHD, MS4A1, CD79A
Canonical Marker Genes: FCER2, TCL1A, IGHM, MS4A1, CD79A
Rationale: The "B Naive” annotation represents the main cluster of naive (antigen-inexperienced) B cells, characterized by a clear and homogeneous expression of key markers including FCER2 (CD23), TCLA1, IGHM, and IGHD. In the “Cell types level 3 20230508” annotation set, this cluster will be further refined and subclustered into 8 distinct subpopulations.
Rationale DOI: 10.1016/j.it.2022.01.003 10.1016/j.immuni.2020.06.013

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