# Test file for FoxJExpressionAssay (in vitro only)
# This assay is IN VITRO ONLY (supported_contexts: in_vitro_only)
# Performed on cell culture systems.
#
# Demonstrates per-condition outputs: the vehicle control record anchors the
# fold-change scale at 1.0 and the PM2.5 record carries the reduced values,
# each linked to its exposure condition via measured_under.
foxj_assays:
  - id: "FOXJ:001"
    name: "FoxJ1 expression after PM2.5 exposure"
    has_exposure_condition:
      - id: "EXPOSURE:foxj-vehicle-24h"
        name: "DMSO vehicle 0.1% for 24 hours (control)"
        exposure_duration:
          value: "24"
          unit:
            id: "UO:0000032"
            name: "hour"
      - id: "EXPOSURE:foxj-pm25-24h"
        name: "PM2.5 10 ug/cm2 for 24 hours"
        exposure_agent:
          id: "ENVO:01000415"
          name: "fine respirable suspended particulate matter"
        exposure_concentration:
          value: "10"
          unit:
            id: "UO:0010071"
            name: "microgram per square centimeter"
        exposure_duration:
          value: "24"
          unit:
            id: "UO:0000032"
            name: "hour"
    has_specified_output:
      - id: "FOXJ:001-output-control"
        name: "Vehicle control FoxJ1 measurements"
        experimental_group: vehicle_control
        measured_under: "EXPOSURE:foxj-vehicle-24h"
        foxj1_mrna_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 3
        foxj1_positive_cell_percentage:
          value: "68"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 3
          variability:
            variability_type: standard_deviation
            value: "4.5"
            unit:
              id: "UO:0000187"
              name: "percent"
        foxj1_protein_expression:
          value: "1.0"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 3
        foxj1_nuclear_localization:
          value: "61"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 3
      - id: "FOXJ:001-output-pm25"
        name: "PM2.5-exposed FoxJ1 measurements"
        experimental_group: treated
        measured_under: "EXPOSURE:foxj-pm25-24h"
        foxj1_mrna_expression:
          value: "0.65"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 3
          variability:
            variability_type: standard_deviation
            value: "0.08"
            unit:
              id: "STATO:0000169"
              name: "fold change"
        foxj1_positive_cell_percentage:
          value: "42"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 3
          variability:
            variability_type: standard_deviation
            value: "5.2"
            unit:
              id: "UO:0000187"
              name: "percent"
        foxj1_protein_expression:
          value: "0.58"
          unit:
            id: "STATO:0000169"
            name: "fold change"
          central_tendency: mean
          sample_size: 3
        foxj1_nuclear_localization:
          value: "35"
          unit:
            id: "UO:0000187"
            name: "percent"
          central_tendency: mean
          sample_size: 3
    assay_date: "2024-09-05"
    informs_on_key_event:
      id: "KE:ke-altered-ciliogenesis"
      name: "Altered ciliogenesis"
      biological_action: decreased
      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'"

# Analysis layer: the fold change reported by the paper, so derivation is
# "reported" rather than computed from the two output records.
response_comparisons:
  - id: "COMP:FOXJ001-mrna"
    name: "Change in FOXJ1 mRNA expression, PM2.5 vs vehicle"
    derived_from_assay: "FOXJ:001"
    compared_measurement: "foxj1_mrna_expression"
    control_output: "FOXJ:001-output-control"
    treated_output: "FOXJ:001-output-pm25"
    change_type: fold_change
    change_direction: decreased
    change_value:
      value: "0.65"
      unit:
        id: "STATO:0000169"
        name: "fold change"
    p_value: 0.01
    statistical_test: "two-sample t-test"
    derivation: reported_in_paper