Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Main

Cell Metadata

B/DZ

Ontology Term: centroblastCL:0009112
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centroblast, germinal center dark zone B cell
Category Class of which the cell type is a subclass.: germinal center B cellCL:0000844
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD79B, STMN1, MKI67, POU2AF1, AICDA
Canonical Marker Genes: BCL6, CXCR4, AID, CD10, CD38, CD77
Rationale: CD79B shows these are B cells POU2AF1 and AICDA are germinal center markers for B cells, and AICDA points towards dark zone. proliferation markers MKI67 and stathmin (STMN1) upregulated when compared to other B cell clusters show these have more of a proliferating signature, which points to dark zone B cells.

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/

Ontology Term: centroblastCL:0009112
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: lymph node centroblast, germinal center dark zone B cell
Category Class of which the cell type is a subclass.: germinal center B cellCL:0000844
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CD79B, STMN1, MKI67, POU2AF1, AICDA
Canonical Marker Genes: BCL6, CXCR4, AID, CD10, CD38, CD77
Rationale: CD79B shows these are B cells POU2AF1 and AICDA are germinal center markers for B cells, and AICDA points towards dark zone. proliferation markers MKI67 and stathmin (STMN1) upregulated when compared to other B cell clusters show these have more of a proliferating signature, which points to dark zone B cells.

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/