B/LZ
- SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.
- lymph node centrocyte, light zone germinal center B cell
- CategoryClass of which the cell type is a subclass.
- germinal center B cellCL:0000844
- Rationale
- CD79A/B and MS4A1 shows these are B cells
RGS13 is the highest DE gene here compared to other B cells, and points to germinal center B. SERPINA9 is specific to germinal center B cells, and is especially prevalent in light zone B cells. CD40 and MARCKSL1 also point to B cell selection pathways.
The expression of RGS and SERPINA9 alongside lack of proliferation markers MKI67 and stathmin (STMN1) upregulated when compared to other B cell clusters point to light zone germinal center Bcells that are undergoing selection.
Inherited from celltype
- Set of Labels Description
- In this paper we used an automated iterative subclustering algorithm to find hundreds of cell state clusters, after which we merged unsupported clusters and annotated each resulting cluster with a better-known cell subtype. The high-res cell state clusters are annotated as subtype.gene1.gene2, so in some cases we didn't directly name some commonly named subtypes, such as pericytes. When we run DE on the resulting subtypes, we find many canonical and scRNA-suggested marker genes.
- Annotation Method
- both
- Algorithm Name
- ARBOL
- Algorithm Version
- v1.0
- Algorithm URL
- https://github.com/jo-m-lab/ARBOL/
