snRNA-seq of human retina - all cells

HAC95

Ontology Term

amacrine cellCL:0000561

Synonyms

Terms that have the same, or nearly the same, meaning as the selected cell type.

ACs, AC, amacrine neuron

Category

Class of which the cell type is a subclass.

GABAergic Glycinergic amacrine cells

Ontology Assessment

Disagreements with any aspect of the Cell Ontology.

The Cell Ontology has two existing terms for two amacrine subclasses: GABAergic amacrine cells (CL:4030027) and Glycinergic amacrine cells (CL:4030028). They have specific markers: GABA-synthetic enzymes GAD1 and GAD2 for GABAergic amacrine cells; glycine transporter SLC6A9 for Glycinergic amacrine cells. However, the Cell Ontology does not have a term for amacrine cells expressing markers for both of these amacrine subclasses. The evidence for the new term is that around 10 amacrine clusters in the Human Retina Cell Atlas highly express markers for both GABAergic and Glycinergic amacrine cells as discussed in the following publications: https://doi.org/10.1038/s41598-020-66092-9 https://doi.org/10.1523/JNEUROSCI.0471-20.2020 The new ontology term of GABAergic Glycinergic amacrine cells should be at the same level as GABAergic amacrine cells (CL:4030027) and Glycinergic amacrine cells (CL:4030028). Its parent term should be CL:0000561, and there is no synonym term for this new term.

Marker Gene Evidence

Gene markers used by researcher to assign this cell annotation.

LINC02306, AC097511.1, LINC00616, RASEF, LGR5, NRP2, RIT2, KCNMB2-AS1, NXPH2, DGKB

Canonical Marker Genes

unknown

Rationale

97.4%Unassigned of the Sanes dataset; 59.0%Unassigned+41.0%Gl5 of the macaque dataset; 97.4%Unassigned of the mouse dataset; Known markers are curated from human, macaque, and mouse markers.

Inherited from author_cell_type

Set of Labels Description

This is the initial cell type label for the atlas annotation. These labels will be examined, refined, and updated during the annotation jamboree.

Annotation Method

manual