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

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Cell Metadata

TA

Ontology Term: transit amplifying cellCL:0009010
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: TACs, transit amplifying progenitor cell, transit-amplifying cell, transient amplifying cell, TAC, TA
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KRT8, KRT18, OLFM4, EPCAM, MKI67
Canonical Marker Genes: PCNA, KRT5, KRT8, CCND1
Rationale: These are clear epithelial cells based on OLFM4, KRT, EPCAM expression, but they also express some proliferative markers like MKI67 compared to other epithelial cells, so we called them transit amplifying

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: transit amplifying cellCL:0009010
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: TACs, transit amplifying progenitor cell, transit-amplifying cell, transient amplifying cell, TAC, TA
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: KRT8, KRT18, OLFM4, EPCAM, MKI67
Canonical Marker Genes: PCNA, KRT5, KRT8, CCND1
Rationale: These are clear epithelial cells based on OLFM4, KRT, EPCAM expression, but they also express some proliferative markers like MKI67 compared to other epithelial cells, so we called them transit amplifying

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/