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

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Cell Metadata

Glial

Ontology Term: glial cellCL:0000125
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: neuroglia, neuroglial cell, glia, enteric glial cell
Category Class of which the cell type is a subclass.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CRYAB, CLU, SPARC, S100B, PLP1
Canonical Marker Genes: S100B, PLP1, GFAP, SOX10
Rationale: Based on CRYAB, SPARC, CLU and PLP1 expression, these appear to be glial cells that are involved in some healing process. PLP1 places them as Glia and the others point to glial roles

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: glial cellCL:0000125
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: neuroglia, neuroglial cell, glia, enteric glial cell
Category Class of which the cell type is a subclass.: stromal cellCL:0000499
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: CRYAB, CLU, SPARC, S100B, PLP1
Canonical Marker Genes: S100B, PLP1, GFAP, SOX10
Rationale: Based on CRYAB, SPARC, CLU and PLP1 expression, these appear to be glial cells that are involved in some healing process. PLP1 places them as Glia and the others point to glial roles

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/