Human Gut Cell Atlas (HGCA) v1 - Lymphoid Lineage

CD4 Naive

Ontology Term: naive T cellCL:0000898
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: naive CD4 T cell, CD4 Tnaive
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.: CD4, CCR7, LEF1, IL7R, KLF2, S1PR5, SELL
Canonical Marker Genes: CCR7, IL7R, SELL
Rationale: CD4 Naive T cells are defined as CCR7, IL7R, LEF1 and SELL expressing signatures

Set of Labels Description: Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.
Annotation Method: both
Algorithm Name: scIB
Algorithm Version: 1.2.1
Algorithm URL: https://github.com/theislab/scib