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

T_unknown

Ontology Term: T cellCL:0000084
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T lymphocyte, T-lymphocyte, T-cell
CategoryClass of which the cell type is a subclass.: peripheral blood mononuclear cellCL:2000001
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3D, CD3G
Canonical Marker Genes: unknown
Rationale: T and NK cells were identified via RCAv2, as well as via cell population-specific integration and sub-clustering. These T cells either had heightened levels of platelet marker gene expression, or could not be confidently annotated as a specific T cell subtype.

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: T cellCL:0000084
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T lymphocyte, T-lymphocyte, T-cell
CategoryClass of which the cell type is a subclass.: peripheral blood mononuclear cellCL:2000001
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: CD3D, CD3G
Canonical Marker Genes: unknown
Rationale: T and NK cells were identified via RCAv2, as well as via cell population-specific integration and sub-clustering. These T cells either had heightened levels of platelet marker gene expression, or could not be confidently annotated as a specific T cell subtype.

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