An Atlas of Cells in the Human Tonsil

Main

Cell Metadata

B activated

Ontology Term: B cellCL:0000236
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: B-cell, B-lymphocyte, 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, IGHD, NFKB2, REL, CD69, MYC, CD83, EGR3, CCL3
Canonical Marker Genes: FCER2, IGHD, NFKB2, REL, CD69, MYC, CD83, EGR3, CCL3
Rationale: Cells in this cluster express typical NBC markers such as FCER2 (CD23), TCLA1, IGHM and IGHD. This cluster is characterized by the expression of very specific genes that seem to correspond to activation and early GC commitment due to the transient MYC upregulation (Dominguez-Sola et al., 2012). For instance, we observed high expression of EGR family (i.e. EGR1, EGR2, EGR3), transcription factors that are rapidly induced upon stimulation of the BCR genes (Gururajan et al., 2008) related to NF-kB pathway (i.e. NFKB1, NFKB2, NFKBIA, NFKBID, RELB) (Burger and Chiorazzi, 2013); or proinflammatory chemokines i.e. CCL3 and CCL4 (Takahashi et al., 2015) . Furthermore, in this cluster we identified high levels of bone-fide activation marker, i.e. CD69 (Cibrián and Sánchez-Madrid, 2017).
Rationale DOI: 10.1038/ni.2428 10.4049/jimmunol.181.7.4590 10.1016/j.it.2013.07.002 10.1111/bjh.13659 10.1002/eji.201646837 10.1016/j.it.2022.01.003 10.1126/sciimmunol.abe6291 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: B cellCL:0000236
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: B-cell, B-lymphocyte, 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, IGHD, NFKB2, REL, CD69, MYC, CD83, EGR3, CCL3
Canonical Marker Genes: FCER2, IGHD, NFKB2, REL, CD69, MYC, CD83, EGR3, CCL3
Rationale: Cells in this cluster express typical NBC markers such as FCER2 (CD23), TCLA1, IGHM and IGHD. This cluster is characterized by the expression of very specific genes that seem to correspond to activation and early GC commitment due to the transient MYC upregulation (Dominguez-Sola et al., 2012). For instance, we observed high expression of EGR family (i.e. EGR1, EGR2, EGR3), transcription factors that are rapidly induced upon stimulation of the BCR genes (Gururajan et al., 2008) related to NF-kB pathway (i.e. NFKB1, NFKB2, NFKBIA, NFKBID, RELB) (Burger and Chiorazzi, 2013); or proinflammatory chemokines i.e. CCL3 and CCL4 (Takahashi et al., 2015) . Furthermore, in this cluster we identified high levels of bone-fide activation marker, i.e. CD69 (Cibrián and Sánchez-Madrid, 2017).
Rationale DOI: 10.1038/ni.2428 10.4049/jimmunol.181.7.4590 10.1016/j.it.2013.07.002 10.1111/bjh.13659 10.1002/eji.201646837 10.1016/j.it.2022.01.003 10.1126/sciimmunol.abe6291 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