# Test file for GeneExpressionAssay (in vitro only)
# This assay is IN VITRO ONLY (supported_contexts: in_vitro_only)
# Performed on cell culture systems
gene_expression_assays:
  - id: "GE:001"
    name: "IL-8 gene expression after exposure"
    target_gene: "PR:000006689"
    has_specified_output:
      id: "GE:001-output"
      name: "GE:001 measurement results"
      mrna_level:
        value: "3.5"
        unit:
          id: "UO:0000193"
          name: "fold change"
      protein_level:
        value: "2.1"
        unit:
          id: "UO:0000193"
          name: "fold change"
      percentage_positive_cells:
        value: "45"
        unit:
          id: "UO:0000187"
          name: "percent"
    gene_expression_method: "qRT-PCR"
    normalization_reference: "GAPDH"
    assay_date: "2024-10-01"
    has_exposure_condition:
      - id: "EXPOSURE:lps-100ng-6h"
        name: "LPS 100 ng/mL for 6 hours"
        exposure_agent:
          id: "CHEBI:16412"
          name: "lipopolysaccharide"
        exposure_concentration:
          value: "100"
          unit:
            id: "UO:0000275"
            name: "nanogram per milliliter"
        exposure_duration:
          value: "6"
          unit:
            id: "UO:0000032"
            name: "hour"
    study_subject:
      subject_type: CellularSystem
      id: "soma:culture-009"
      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: 21
      donor_info: "Healthy donor, non-smoker, age 40"
      replicates_per_donor: 3
      substrate_type: transwell_insert
      passage_number: 2
    follows_protocols:
      - protocol_type: MolecularAssayProtocol
        id: "PROTOCOL:qpcr-002"
        name: "qRT-PCR for cytokine expression"
        detection_method: "TaqMan qPCR"
        reference_gene: "GAPDH"
        platform: "QuantStudio 6"