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

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Cell Metadata

Prolif/Secretory

Ontology Term: secretory cellCL:0000151
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: OLFM4, REG1A, REG1B, SPINK1, EPCAM, KRT18, STMN1
Canonical Marker Genes: TFF3, MUC2, KRT5
Rationale: Similar to the other "secretory" cluster, these are clear epithelial cells displaying SPINK1 and REG1A/B, but these also display STMN1 and other cell cycle markers.

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: secretory cellCL:0000151
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: unknown
CategoryClass of which the cell type is a subclass.: epithelial cellCL:0000066
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: OLFM4, REG1A, REG1B, SPINK1, EPCAM, KRT18, STMN1
Canonical Marker Genes: TFF3, MUC2, KRT5
Rationale: Similar to the other "secretory" cluster, these are clear epithelial cells displaying SPINK1 and REG1A/B, but these also display STMN1 and other cell cycle markers.

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/