HCA Gut Cell Atlas v1 Stromal Lineage

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Cell Metadata

Fibroblasts Lamina propria (S1)

Ontology Term: intestinal lamina propria fibroblastCL:4047023
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ADAMDEC1, ABCA8, FABP4
Canonical Marker Genes: PDPN, COL1A1, DCN
Rationale: This label represents superficial lamina propria fibroblasts that are ADAMDEC1+, ABCA8+, FABP4+ and form the dominant fibroblast population across datasets and samples. FOS+ Fibroblast Lamina propria or Ribo(high) Fibroblast Lamina propria, and note an upper-lamina WNT4+ subset (Stroma_0_2) described in the literature, as well as plasma (IGHA+) and myeloid (C1S/C1R+) doublet-contaminated clusters. Taken together, the transcriptional program, high dataset and sample diversity, and literature on WNT4+ villus-oriented fibroblasts support a high-confidence lamina propria fibroblast identity, with FOS and ribosomal signatures reflecting activation state rather than separate cell types.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools

Ontology Term: intestinal lamina propria fibroblastCL:4047023
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: unknown
Category Class of which the cell type is a subclass.: fibroblastCL:0000057
Ontology Assessment Disagreements with any aspect of the Cell Ontology.: —
Marker Gene Evidence Gene markers used by researcher to assign this cell annotation.: ADAMDEC1, ABCA8, FABP4
Canonical Marker Genes: PDPN, COL1A1, DCN
Rationale: This label represents superficial lamina propria fibroblasts that are ADAMDEC1+, ABCA8+, FABP4+ and form the dominant fibroblast population across datasets and samples. FOS+ Fibroblast Lamina propria or Ribo(high) Fibroblast Lamina propria, and note an upper-lamina WNT4+ subset (Stroma_0_2) described in the literature, as well as plasma (IGHA+) and myeloid (C1S/C1R+) doublet-contaminated clusters. Taken together, the transcriptional program, high dataset and sample diversity, and literature on WNT4+ villus-oriented fibroblasts support a high-confidence lamina propria fibroblast identity, with FOS and ribosomal signatures reflecting activation state rather than separate cell types.

Set of Labels Description: Cell annotations (Prelim annotation) are based on the finest possible label that could be used to describe each of the ~500 clusters found during integration and subclustering
Annotation Method: both
Algorithm Name: scVI
Algorithm Version: 1.3.2
Algorithm URL: https://github.com/scverse/scvi-tools