object_id: "SC:v1.0.0-database-resource:CPEB1:1.5-DRAFT"
card_schema: "nmd-vcell-study-card/1.5"
card_version: "1.5"
resource_release: "v1.0.0-database-resource"
evidence_freeze: "2026-07-25"
interface_build: "EA-20260729-17"
gene: "CPEB1"
card_type: "expression_verification"
current_action_code: "verify_expression"
current_action: "Verify expression"
lifecycle:
  state: "DRAFT"
  revision: 1
  immutable: false
  registered_at: null
  supersedes: null
  immutable_after_registration: true
decision_blocking_gap:
  code: "GAP-06"
  label: "Expression feasibility is not verified in the intended model"
highest_missing_evidence_layer: "L4_dmd_functional_validation"
secondary_gaps:
  - "GAP-02 independent muscle-context perturbation"
  - "GAP-03 DMD-relevant functional validation"
  - "GAP-07 independent replication"
frozen_evidence_snapshot:
  snapshot_schema: "nmd-vcell-study-card-frozen-evidence-snapshot/1.0"
  source_record: "gene/CPEB1"
  highest_supported_level: "L2_observed_same_context_perturbation"
  highest_assessed_level: "L2_observed_same_context_perturbation"
  observed_hepg2_perturbation:
    assessment_status: "assessed"
    support_status: "supported"
    observed_cells: 100
  external_context_screen:
    assessment_status: "not_assessed"
    support_status: null
    hit: null
    effect_size: null
    fdr: null
    interpretation: null
  dmd_prior:
    integrated_prior_direction: "up"
    source_direction_state: "conflicted"
    source_agreement_proportion: 0.6666666666666666
    agreeing_sources: 2
    assessed_sources: 3
    coverage_state: "3_of_4_sources"
    uncertainty_state: "direction_conflict_retained"
  context_metrics:
    skeletal_muscle_median_tpm: 0.731389
    depmap_median_gene_effect: -0.0705167717127638
    moderate_dependency_flag: false
  visual_boundary: "Descriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated."
unresolved_question: "Is CPEB1 detectably expressed at RNA and protein level in the intended human myogenic state?"
biological_context: "Intended human myoblast/myotube model; healthy, DMD or isogenic status must be declared before registration."
perturbation_modality: "No perturbation escalation. Verify RNA by qPCR/ddPCR and protein by an orthogonal assay where a validated reagent exists."
comparator_and_controls:
  - "No-template and no-reverse-transcriptase controls."
  - "Positive-expression tissue/cell control."
  - "Housekeeping genes and assay-specific protein control."
primary_endpoint: "Predeclared RNA detectability and, where feasible, protein detectability in the intended cell state."
secondary_endpoints:
  - "Myoblast-to-myotube expression change."
  - "Between-donor expression heterogeneity."
  - "Assay limit of detection and quantification."
primary_estimand: "Mean log-scale expression in the intended state and the proportion of independent biological replicates above the predeclared detection threshold."
state_transition_design:
  scientific_object: "perturbation × cell state × disease context × time × phenotype"
  mechanism_hypothesis: "Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence."
  cell_context_fields:
    disease_background: "Required before registration: healthy, DMD or isogenic corrected."
    myogenic_state: "Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube."
    donor_or_isogenic_pair: "Required before registration; preserve donor-specific estimates."
  timepoint_plan:
    - "[object Object]"
    - "[object Object]"
    - "[object Object]"
  endpoint_domains:
    target_engagement:
      - "mRNA"
      - "protein where validated"
      - "perturbation efficiency"
    functional:
      - "fusion"
      - "morphology"
      - "membrane integrity"
      - "calcium"
      - "contraction"
    safety:
      - "viability"
      - "proliferation"
      - "differentiation blockade"
      - "global stress"
    replication:
      - "reagent"
      - "donor or isogenic pair"
      - "future batch"
  cell_cell_consequence:
    current_status: "not_assessed"
    future_levels:
      - "conditioned medium"
      - "two-cell co-culture"
      - "three-dimensional muscle model"
      - "spatial perturbation model"
  response_archetype:
    current_status: "not_assessed"
    allowed_values:
      - "robust_responder"
      - "dmd_specific_responder"
      - "donor_variable"
      - "state_specific"
      - "toxic_responder"
      - "null_with_equivalence_margin"
      - "discordant"
      - "qc_failure"
      - "inconclusive"
perturbation_direction_rationale:
  selected_hypothesis: "unresolved_requires_registration"
  allowed_hypotheses:
    - "activation"
    - "inhibition"
    - "bidirectional_exploration"
    - "direction_not_identifiable"
  required_justification: "State whether the disease-associated direction is hypothesized as causal, compensatory or accompanying, and preserve the opposite-direction alternative. DMD direction and counteralignment never choose an intervention automatically."
minimally_important_effect: "Required before registration; derive from assay biology or a justified pilot and store the numeric value with units."
negligible_effect_margin: "Required before interpreting a null result; store a symmetric or asymmetric numeric margin with units."
suggested_sample_size_range: "3–6 independent biological replicates/donors per intended state as a planning range; final n requires variance-based power analysis."
randomisation_unit: "Independent culture/donor allocation to assay batch."
blocking_factors:
  - "Donor or isogenic pair."
  - "Differentiation batch."
  - "Assay plate."
statistical_model: "Linear mixed model on log expression with state fixed effect and donor/batch random intercepts when supported."
multiple_testing_family: "Primary gene × assay endpoints declared on this card; adjust secondary panels separately."
missing_data_rule: "Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis."
assay_qc_thresholds:
  - "Numeric RNA/protein detection thresholds must be filled before registration."
  - "Replicate CV and amplification-efficiency limits must be assay validated."
guide_concordance_rule: "Not applicable until a perturbation study is registered."
donor_replication_rule: "The expression gate must be met in at least two independent biological replicates and not be driven by one donor."
estimated_time_band: "2–4 weeks after assay setup; planning estimate only."
estimated_cost_band: "Institution- and assay-dependent; obtain a local itemised quote before registration."
preregistration_status: "draft_requires_direction_rationale_numeric_effect_margin_sample_size_and_qc_thresholds"
inferential_unit: "Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates."
evidence_import_requirements: []
planning_fields_not_applicable: []
stop_rules:
  - "Stop or classify as infeasible if a required numeric QC threshold fails."
  - "Do not interpret a nonsignificant result as no material effect without a negligible-effect interval."
  - "Do not change canonical candidate status automatically; require governed review."
escalation_rule: "Escalate from L2 to L3b only after independent context-matched perturbation replication; L4 requires replicated DMD-relevant muscle evidence."
evidence_transition: "Current evidence state → predeclared independent test → governed evidence-level review."
data_release_plan: "Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card."
boundary: "This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation."
stable_url: "study-card/CPEB1"
exports:
  json: "api/v1.1/study-cards/CPEB1.json"
  yaml: "downloads/study-cards/CPEB1.yaml"
  tsv: "downloads/study-cards/CPEB1.tsv"
