Integrated Human Breast Cell Atlas v1.0 - all cells

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Cell Metadata

T-lymphocyte

Ontology Term: T cellCL:0000084
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: T cell, T-cell
Category Class of which the cell type is a subclass.: lymphocyteCL:0000542
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: The 'T-lymphocyte' grouping includes NK/NKT cells (CL:0000623) alongside CD4+ and CD8+ T cells. NK cells are not strictly T lymphocytes; CL:0000084 (T cell) is used as the practical broad label for this lymphoid immune compartment.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: GNLY, NKG7, GZMK, RGS1, GZMH, CCL20, KLRB1, RIPOR2, TRAC
Canonical Marker Genes: CD3D, CD3E, CD3G, TRAC, CD4, CD8A
Rationale: The 'T-lymphocyte' group was identified and annotated by Austin Reed, encompassing CD4+ T cells, CD8+ T cells, and NK/NKT cells. CD3D, CD3E, and TRAC are canonical pan-T cell markers used for identification.
Rationale DOI: 10.1038/s41588-024-01688-9 10.1038/s41586-023-06252-9

Set of Labels Description: Cell annotations based on resolution broad clustering using the Leiden algorithm.
Annotation Method: manual

Ontology Term: T cellCL:0000084
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: T cell, T-cell
Category Class of which the cell type is a subclass.: lymphocyteCL:0000542
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: The 'T-lymphocyte' grouping includes NK/NKT cells (CL:0000623) alongside CD4+ and CD8+ T cells. NK cells are not strictly T lymphocytes; CL:0000084 (T cell) is used as the practical broad label for this lymphoid immune compartment.
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: GNLY, NKG7, GZMK, RGS1, GZMH, CCL20, KLRB1, RIPOR2, TRAC
Canonical Marker Genes: CD3D, CD3E, CD3G, TRAC, CD4, CD8A
Rationale: The 'T-lymphocyte' group was identified and annotated by Austin Reed, encompassing CD4+ T cells, CD8+ T cells, and NK/NKT cells. CD3D, CD3E, and TRAC are canonical pan-T cell markers used for identification.
Rationale DOI: 10.1038/s41588-024-01688-9 10.1038/s41586-023-06252-9

Set of Labels Description: Cell annotations based on resolution broad clustering using the Leiden algorithm.
Annotation Method: manual