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

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Cell Metadata

Prolif/EC

Ontology Term: epithelial cellCL:0000066
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: epitheliocyte
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: REG1A, KRT8, STMN1, UBE2C, TOP2A, EPCAM
Canonical Marker Genes: VIL1, KRT20, EPCAM
Rationale: These have high KRT8 and EPCAM as well as when compared to other EC, high histone and cell cycle machinery expression (STMN1, H2AFZ, TOP2A, UBE2C).

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: epithelial cellCL:0000066
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: epitheliocyte
Category Class of which the cell type is a subclass.: epithelial cellCL:0000066
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: REG1A, KRT8, STMN1, UBE2C, TOP2A, EPCAM
Canonical Marker Genes: VIL1, KRT20, EPCAM
Rationale: These have high KRT8 and EPCAM as well as when compared to other EC, high histone and cell cycle machinery expression (STMN1, H2AFZ, TOP2A, UBE2C).

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/