# Test file for FoxJExpressionAssay (in vitro only)
# This assay is IN VITRO ONLY (supported_contexts: in_vitro_only)
# Performed on cell culture systems
foxj_assays:
  - id: "FOXJ:001"
    name: "FoxJ1 mRNA expression"
    has_specified_output:
      id: "FOXJ:001-output"
      name: "FOXJ:001 measurement results"
      foxj1_mrna_expression:
        value: "0.65"
        unit:
          id: "UO:0000193"
          name: "fold change"
      foxj1_positive_cell_percentage:
        value: "42"
        unit:
          id: "UO:0000187"
          name: "percent"
      foxj1_protein_expression:
        value: "0.58"
        unit:
          id: "UO:0000193"
          name: "fold change"
      foxj1_nuclear_localization:
        value: "35"
        unit:
          id: "UO:0000187"
          name: "percent"
    assay_date: "2024-09-05"
    informs_on_key_event:
      id: "KE:ke-altered-ciliogenesis"
      name: "Altered ciliogenesis"
      biological_action: altered
      level_of_biological_organization: cellular
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-008"
      name: "Primary HBE ALI culture"
      cell_type:
        id: "CL:0002328"
        name: "bronchial epithelial cell"
      model_species:
        id: "NCBITaxon:9606"
        name: "Homo sapiens"
      primary_cell:
        id: "CL:0002328"
        name: "bronchial epithelial cell"
      anatomical_origin:
        id: "UBERON:0002031"
        name: "bronchus"
      cell_culture_growth_mode: air_liquid_interface
      days_at_differentiation: 14
      donor_info: "Healthy donor, non-smoker"
      replicates_per_donor: 3
      substrate_type: transwell_insert
      passage_number: 2
    follows_protocols:
      - protocol_type: MolecularAssayProtocol
        id: "PROTOCOL:qpcr-001"
        name: "qRT-PCR for FoxJ1"
        detection_method: "SYBR Green qPCR"
        reference_gene: "GAPDH"
        primer_sequences:
          - "FOXJ1-F: 5'-CAGGCCCAGAACTTTCTCC-3'"
          - "FOXJ1-R: 5'-GGCCTTTGGTACTGTCTCAC-3'"