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

ILC

Ontology Term: innate lymphoid cellCL:0001065
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
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.: KIT, TTLL10, TNFRSF18, KLRB1
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 non-CD4+ T cells as well as ILC and NK cells, and these cells were further integrated and sub-clustered. These ILC clusters were manually annotated based on expression of marker genes, as well as by the low numbers 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: innate lymphoid cellCL:0001065
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
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.: KIT, TTLL10, TNFRSF18, KLRB1
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 non-CD4+ T cells as well as ILC and NK cells, and these cells were further integrated and sub-clustered. These ILC clusters were manually annotated based on expression of marker genes, as well as by the low numbers 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