Genes expected to be absent, or expressed at a notably low level, in these cells, and whose absence supports the assignment of this cell annotation.
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Rationale
S2B fibroblasts are positioned toward the crypt top or villus tip and are characterized by NRG1 and NPY, we also highlight VEGFD and TRPA1 as convincing markers of villus-tip subepithelial fibroblasts. Clusters annotated as Fibroblasts Crypt Top (S2B) (for example Stroma_1_1 and 12_1–12_4) show these markers along with the broader S2 program and are present in multiple datasets, albeit with varying mitochondrial content and dataset diversity. We therefore treat S2B as a robust positional subtype of S2, capturing villus-tip fibroblasts with strong NRG1/VEGFD/TRPA1 signatures.
Inherited from hgca_celltype_v1
Set of Labels Description
Cell annotations based on two rounds of subclustering with scVI integration, sample_id as batch key. Cell annotations were refined by expert feedback based on "prelim annotation" on CAP. Prelim annotation is renamed "hgca_celltype_v0" here and the feedback on the "prelim annotation" is available by selecting a previous version of the Integrated Human Gut Atlas on CAP.
