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.
—
Rationale
S2A fibroblasts sit near the crypt base and are enriched for VSTM2A together with PDGFRA, BMP4, WNT5A, POSTN and other S2 markers. Several clusters annotated as Fibroblasts Crypt Bottom (S2A) show very low dataset diversity but reproducible expression of POSTN, F3 and BMPs, and differences between individual S2A annotation clusters are subtle (see annotation_cluster) and may largely reflect activation and quality flags (for example high mitochondrial content) rather than true subtypes. We therefore annotate a single S2A cell type corresponding to crypt-bottom fibroblasts with high-confidence positional identity and variable activation 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.
