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

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Cell Metadata

T/NK/ILC

Ontology Term: T cellCL:0000084
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T-lymphocyte, immature T cell, T-cell, mature T cell, T lymphocyte
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: TRAC, CD3D, TRBC1, CD3E, LEF1, RPS12, RPL22, CCR7, RPS29
Canonical Marker Genes: TRAC, CD3
Rationale: These are lymphocytes with some TRAC/CD3 expression which are differentially high in ribosomal proteins, it can be hard to tell if they are T, NK, or ILC

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: T cellCL:0000084
SynonymsTerms that have the same, or nearly the same, meaning as the selected cell type.: T-lymphocyte, immature T cell, T-cell, mature T cell, T lymphocyte
CategoryClass of which the cell type is a subclass.: T cellCL:0000084
Marker Gene EvidenceGene markers used by researcher to assign this cell annotation.: TRAC, CD3D, TRBC1, CD3E, LEF1, RPS12, RPL22, CCR7, RPS29
Canonical Marker Genes: TRAC, CD3
Rationale: These are lymphocytes with some TRAC/CD3 expression which are differentially high in ribosomal proteins, it can be hard to tell if they are T, NK, or ILC

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/