object_id	card_schema	card_version	resource_release	evidence_freeze	interface_build	gene	card_type	current_action_code	current_action	lifecycle	decision_blocking_gap	highest_missing_evidence_layer	secondary_gaps	frozen_evidence_snapshot	unresolved_question	biological_context	perturbation_modality	comparator_and_controls	primary_endpoint	secondary_endpoints	primary_estimand	state_transition_design	perturbation_direction_rationale	minimally_important_effect	negligible_effect_margin	suggested_sample_size_range	randomisation_unit	blocking_factors	statistical_model	multiple_testing_family	missing_data_rule	assay_qc_thresholds	guide_concordance_rule	donor_replication_rule	estimated_time_band	estimated_cost_band	preregistration_status	inferential_unit	evidence_import_requirements	planning_fields_not_applicable	stop_rules	escalation_rule	evidence_transition	data_release_plan	boundary	stable_url	exports
SC:v1.0.0-database-resource:DNAAF3:1.5-DRAFT	nmd-vcell-study-card/1.5	1.5	v1.0.0-database-resource	2026-07-25	EA-20260729-15	DNAAF3	expression_verification	verify_expression	Verify expression	{"state":"DRAFT","revision":1,"immutable":false,"registered_at":null,"supersedes":null,"immutable_after_registration":true}	{"code":"GAP-06","label":"Expression feasibility is not verified in the intended model"}	L4_dmd_functional_validation	GAP-02 independent muscle-context perturbation | GAP-03 DMD-relevant functional validation | GAP-07 independent replication	{"snapshot_schema":"nmd-vcell-study-card-frozen-evidence-snapshot/1.0","source_record":"gene/DNAAF3","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":115},"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":"consistent_up","source_agreement_proportion":1,"agreeing_sources":1,"assessed_sources":1,"coverage_state":"1_of_4_sources","uncertainty_state":"incomplete_source_coverage"},"context_metrics":{"skeletal_muscle_median_tpm":0.0755557,"depmap_median_gene_effect":0.0598274924538474,"moderate_dependency_flag":false},"visual_boundary":"Descriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated."}	Is DNAAF3 detectably expressed at RNA and protein level in the intended human myogenic state?	Intended human myoblast/myotube model; healthy, DMD or isogenic status must be declared before registration.	No perturbation escalation. Verify RNA by qPCR/ddPCR and protein by an orthogonal assay where a validated reagent exists.	No-template and no-reverse-transcriptase controls. | Positive-expression tissue/cell control. | Housekeeping genes and assay-specific protein control.	Predeclared RNA detectability and, where feasible, protein detectability in the intended cell state.	Myoblast-to-myotube expression change. | Between-donor expression heterogeneity. | Assay limit of detection and quantification.	Mean log-scale expression in the intended state and the proportion of independent biological replicates above the predeclared detection threshold.	{"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":[{"window":"6–12 h","role":"early molecular or signalling response","status":"planning_default_requires_assay_calibration"},{"window":"24–48 h","role":"regulatory program and cell-state transition","status":"planning_default_requires_assay_calibration"},{"window":"4–7 d","role":"differentiation and functional phenotype","status":"planning_default_requires_assay_calibration"}],"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"]}}	{"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."}	Required before registration; derive from assay biology or a justified pilot and store the numeric value with units.	Required before interpreting a null result; store a symmetric or asymmetric numeric margin with units.	3–6 independent biological replicates/donors per intended state as a planning range; final n requires variance-based power analysis.	Independent culture/donor allocation to assay batch.	Donor or isogenic pair. | Differentiation batch. | Assay plate.	Linear mixed model on log expression with state fixed effect and donor/batch random intercepts when supported.	Primary gene × assay endpoints declared on this card; adjust secondary panels separately.	Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.	Numeric RNA/protein detection thresholds must be filled before registration. | Replicate CV and amplification-efficiency limits must be assay validated.	Not applicable until a perturbation study is registered.	The expression gate must be met in at least two independent biological replicates and not be driven by one donor.	2–4 weeks after assay setup; planning estimate only.	Institution- and assay-dependent; obtain a local itemised quote before registration.	draft_requires_direction_rationale_numeric_effect_margin_sample_size_and_qc_thresholds	Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.			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.	Escalate from L2 to L3b only after independent context-matched perturbation replication; L4 requires replicated DMD-relevant muscle evidence.	Current evidence state → predeclared independent test → governed evidence-level review.	Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card.	This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation.	study-card/DNAAF3	{"json":"api/v1.1/study-cards/DNAAF3.json","yaml":"downloads/study-cards/DNAAF3.yaml","tsv":"downloads/study-cards/DNAAF3.tsv"}