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
These fibroblasts are defined by DPT, C7, KCNN3, CA8 and PLCB4 expression and were initially annotated as Muscularis Propria fibroblasts in the hierarchy, but our experts repeatedly note that some clusters with this label are present in many biopsy-derived datasets, which is difficult to reconcile with a strictly muscularis-only population. Marker profiles suggest a deeper S3-like or muscle-adjacent fibroblast population, but current spatial evidence is insufficient to cleanly separate muscularis propria fibroblasts from subserosal or submucosal fibroblasts in the integrated data. We therefore keep this label as a provisional deeper muscle-layer fibroblast class with moderate confidence and flag the spatial assignment as uncertain. Do we need a "deep S3" sub-label?
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.
