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            "description": "The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states. Overall design: A total of 16 breast samples were assayed (4 samples from reductive mammoplasties and 12 from prophylactic mastectomies).",
            "id": "SRP329970"
          },
          "id": "SRX11559757"
        },
        "annotation": {
          "rawDataCondition": {
            "anatEntity": {
              "id": "UBERON:0005200",
              "name": "thoracic mammary gland"
            },
            "anatEntityAuthorAnnotation": "Mammary tissue",
            "cellType": {
              "id": "CL:0002325",
              "name": "mammary alveolar cell"
            },
            "cellTypeAuthorAnnotation": "AP",
            "devStage": {
              "id": "HsapDv:0000133",
              "name": "39-year-old stage (human)"
            },
            "devStageAuthorAnnotation": "39",
            "sex": "female",
            "strain": "White",
            "time": "NA",
            "timeUnit": "NA",
            "species": {
              "id": 9606,
              "name": "human",
              "genus": "Homo",
              "speciesName": "sapiens",
              "preferredDisplayOrder": 1
            }
          },
          "physiologicalStatus": "NA"
        },
        "pipelineSummary": {
          "meanRefIntergenicDistribution": 0.357848,
          "sdRefIntergenicDistribution": 3.063986,
          "pValueThreshold": 0.0500,
          "allUMIsCount": 0,
          "mappedUMIsCount": 16127597,
          "distinctRankCount": 3932,
          "maxRank": 27329.50
        },
        "barcode": ""
      }
    ],
    "downloadUrls": [
      {
        "text": "scRNA-Seq droplet-based processed expression values per cell population in Homo sapiens",
        "href": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Homo_sapiens/Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP329970.tsv.gz",
        "title": "Homo_sapiens_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP329970.tsv.gz"
      },
      {
        "text": "scRNA-Seq droplet-based H5AD data per cell in Homo sapiens",
        "href": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Homo_sapiens/Homo_sapiens_SRP329970_droplet_based.h5ad",
        "title": "Homo_sapiens_SRP329970_droplet_based.h5ad"
      }
    ]
  }
}