Human Breast Cell Atlas (HBCA)

FB1

Ontology Term: fibroblast of breastCL:4006000
Synonyms Terms that have the same, or nearly the same, meaning as the selected cell type.: breast fibroblast
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.: DCN, LUM, COL1A2, VEGFD, CNTN1, ABCA10, MXRA5, CAPN6, SCARA5, DNM1, COL1A1, PDGFD, ABCA9, CCL11
Canonical Marker Genes: DCN, LUM
Negative Marker Genes 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: DCN and LUM used to define the Fibroblast population as supported by the literature. Selected specific markers for this cluster are COL1A2 and VEGFD. Differential expression analysis was performed for each of the level2 cell types and here we report the top 10 markers as determined by one-vs-all negative binomial testing (non-redundant).

Set of Labels Description: This dataset generates a comprehensive Human Breast Cell Atlas (HBCA) using scRNA-seq of over 800,000 cells from 55 donors, identifying 41 cell subclusters across the epithelial (LASP, LHS, BMYO), immune (T cells, NK, B cells, macrophages), and stromal (fibroblast, endothelial, perivascular) compartments. To capture how key risk-modifying factors alter the homeostatic cellular composition of the breast, we assembled a cohort with broad donor diversity spanning a wide range of ages, parity statuses, and germline mutation backgrounds. By annotating at this resolution we could apply differential abundance testing to detect subcluster-level compositional shifts associated with each risk factor. This annotation set also serves as a standardised reference taxonomy, enabling harmonised cell-type comparisons across existing datasets where nomenclature had been inconsistent.
Annotation Method: manual