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
EPCAM, CDH1 and KRT17 used to define the epithelial population, further refined by KIT, ALDH1A3 and SLPI to define the luminal adaptive secretory precursor cells of mammary gland (LASP), as supported by literature. Selected specific markers for this cluster (LASP2) are KRT16 and KRT6B. 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).
Inherited from level2
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.
