AIDA Phase 1 Data Freeze v2: Chinese, Indian, Japanese, Korean, Malay, and Thai donors in Japan, Singapore, South Korea, Thailand, and India

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Cell Metadata

CD4+_T_cyt

Ontology Term: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: CD4-positive, alpha-beta cytotoxic T lymphocyte, CD4-positive, alpha-beta cytotoxic T-cell, CD4-positive, alpha-beta cytotoxic T-lymphocyte
Category Class of which the cell type is a subclass.: CD4-positive, alpha-beta T cellCL:0000624
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD3D, CD3G, CD4, ITGB1, KLRB1, CCL5, GZMA, GZMB, GZMH, GNLY, FGFBP2
Canonical Marker Genes: unknown
Rationale: T and NK cells were identified via RCAv2. Integration and sub-clustering of all NK and T cells were performed to identify CD4+ T cells, and CD4+ T and dnT cells were further sub-clustered. CD4+ T clusters were annotated based on marker genes, particularly heightened levels of GZMB expression, as well as the presence of TCR barcodes.

Set of Labels Description: These author cell type labels were assigned largely at the per-cluster level. We identified broad cell types using RCAv2-based clustering (B, CD34+ haematopoietic stem and progenitor cell (HSPC), myeloid, natural killer (NK), plasma cell, plasmacytoid dendritic cell (pDC), platelet, and T). We then performed cell population-specific (B; myeloid + pDC; CD4+ T and dnT; non-CD4+ T and NK and ILC) integration (Seurat RPCA) and sub-clustering (Louvain clustering), and annotated clusters based on their marker genes.
Annotation Method: manual

Ontology Term: CD4-positive, alpha-beta cytotoxic T cellCL:0000934
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: CD4-positive, alpha-beta cytotoxic T lymphocyte, CD4-positive, alpha-beta cytotoxic T-cell, CD4-positive, alpha-beta cytotoxic T-lymphocyte
Category Class of which the cell type is a subclass.: CD4-positive, alpha-beta T cellCL:0000624
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD3D, CD3G, CD4, ITGB1, KLRB1, CCL5, GZMA, GZMB, GZMH, GNLY, FGFBP2
Canonical Marker Genes: unknown
Rationale: T and NK cells were identified via RCAv2. Integration and sub-clustering of all NK and T cells were performed to identify CD4+ T cells, and CD4+ T and dnT cells were further sub-clustered. CD4+ T clusters were annotated based on marker genes, particularly heightened levels of GZMB expression, as well as the presence of TCR barcodes.

Set of Labels Description: These author cell type labels were assigned largely at the per-cluster level. We identified broad cell types using RCAv2-based clustering (B, CD34+ haematopoietic stem and progenitor cell (HSPC), myeloid, natural killer (NK), plasma cell, plasmacytoid dendritic cell (pDC), platelet, and T). We then performed cell population-specific (B; myeloid + pDC; CD4+ T and dnT; non-CD4+ T and NK and ILC) integration (Seurat RPCA) and sub-clustering (Louvain clustering), and annotated clusters based on their marker genes.
Annotation Method: manual