HCA Gut Cell Atlas v1 Lymphoid Lineage

Main

Cell Metadata

CD8 TRM

Ontology Term: Tc17 cellCL:0002128
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: TRM, tissue resident memory CD8 T cell
Category Class of which the cell type is a subclass.: CD8-positive, alpha-beta T cellCL:0000625
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD8A, CD8B, ITGAE, CD69, ITGA1, RORA
Canonical Marker Genes: ITGAE, CD69, ITGA1
Rationale: ITGAE and RORA point to granzyme positive t resident memory populations, and clusters of these tend to be more unique to certain sections of the gut, driving down the number of datasets they are found in (dataset diversity metric)

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools

Ontology Term: Tc17 cellCL:0002128
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: TRM, tissue resident memory CD8 T cell
Category Class of which the cell type is a subclass.: CD8-positive, alpha-beta T cellCL:0000625
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD8A, CD8B, ITGAE, CD69, ITGA1, RORA
Canonical Marker Genes: ITGAE, CD69, ITGA1
Rationale: ITGAE and RORA point to granzyme positive t resident memory populations, and clusters of these tend to be more unique to certain sections of the gut, driving down the number of datasets they are found in (dataset diversity metric)

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools