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
Submucosal S3 fibroblasts occupy deeper layers and crypt base regions and are enriched for GREM1, C7, OLFM4, PTGS2, THY1, SEMA3A and GLI1, consistent with crypt-support or trophocyte roles. Cluster-level annotations describe RSPO3, GREM1, DCN and C3 as strong markers of submucosal fibroblasts (for example Stroma_2_0) and we note that S3 populations have lower dataset diversity and appear deeper than lamina propria fibroblasts, especially in resection-derived data. Multiple clusters labeled as Fibroblasts Submucosal (aka Crypt Support/Trophocytes/S3) recur with similar signatures, supporting a distinct S3 fibroblast class even though a dedicated CL term is still needed.
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.
