{ "plan_id": "EXPERIMENT-PLAN:DMD:ZNF133:CRISPRI:48H:FUSION_AND_MOLECULAR_RESPONSE:V1", "version": "1.0.0", "lifecycle_track": "TRUTH_GENERATION", "overall_state": "DRAFT_BLOCKED_OPEN_NUMERIC_AND_AUTHORITY_GATES", "source_answer_id": "ANSWER:Q2:DMD:PROLIFERATING_MYOBLAST:CRISPRI:ZNF133:48H:FUSION_AND_MOLECULAR_RESPONSE:V1", "source_answer_sha256": "5f3a8032becd59203d545af781bf5ac28e0d2a9b36716ce6e6e3ef1c7e4b80c4", "study_card_id": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "study_card_path": "/resource/study-card/ZNF133", "study_card_source_sha256": "844ebfb33670f731dbfb5ecb4e3f3507b58402116c18968f461e37c78c0b49f9", "question": { "question_schema": "nmd-vcell-research-question/2.0", "query_version": "2", "question_id": "Q2:DMD:PROLIFERATING_MYOBLAST:CRISPRI:ZNF133:48H:FUSION_AND_MOLECULAR_RESPONSE:SINGLE", "disease": "DMD", "cell_state": "PROLIFERATING_MYOBLAST", "perturbation": "CRISPRI", "target": "ZNF133", "targets": [ "ZNF133" ], "time": "48H", "endpoint": "FUSION_AND_MOLECULAR_RESPONSE", "study_mode": "SINGLE_TARGET" }, "execution_authorized": false, "registration_ready": false, "prediction_required": false, "gate_summary": { "ready": 6, "partial": 2, "open": 6, "total": 14 }, "gates": [ { "gate_id": "GATE:QUESTION_SCOPE", "label": "Question scope", "class": "READY", "state": "READY_REGISTERED_ANSWER", "source": "ANSWER:Q2:DMD:PROLIFERATING_MYOBLAST:CRISPRI:ZNF133:48H:FUSION_AND_MOLECULAR_RESPONSE:V1", "requirement": "Preserve the exact disease, cell state, perturbation, target, time and endpoint identity." }, { "gate_id": "GATE:BIOLOGICAL_SCOPE", "label": "Disease, cell, target, time and endpoint", "class": "READY", "state": "READY_AS_DRAFT", "source": "Q2:DMD:PROLIFERATING_MYOBLAST:CRISPRI:ZNF133:48H:FUSION_AND_MOLECULAR_RESPONSE:SINGLE", "requirement": "Freeze the query-selected scope at registration; do not generalize beyond it." }, { "gate_id": "GATE:PRIMARY_ESTIMAND", "label": "Primary estimand", "class": "PARTIAL", "state": "PARTIAL_REQUIRES_ENDPOINT_SCALE_AND_NUMERIC_EFFECT", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Choose the primary endpoint scale and freeze the minimally important numeric effect with units." }, { "gate_id": "GATE:INFERENTIAL_UNIT", "label": "Inferential unit", "class": "READY", "state": "READY_AS_DRAFT", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates." }, { "gate_id": "GATE:CONTROLS", "label": "Comparator and controls", "class": "READY", "state": "READY_AS_DRAFT", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Non-targeting control. Positive assay control. Mock delivery control when delivery itself can affect phenotype. Target-engagement and viability controls." }, { "gate_id": "GATE:REPLICATION", "label": "Replication and sample size", "class": "OPEN", "state": "OPEN_POWER_CALCULATION", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Use the 3–6 replicate range only for a variance pilot; freeze final n after assay variance and minimally important effect are available." }, { "gate_id": "GATE:RANDOMIZATION", "label": "Randomization and blocking", "class": "PARTIAL", "state": "PARTIAL_SEQUENCE_NOT_GENERATED", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Randomize Independent culture well or biological replicate, not individual cells.; retain blocks for Donor/isogenic pair. Differentiation batch. Plate and reagent identity.; generate and freeze the allocation sequence." }, { "gate_id": "GATE:BLINDING", "label": "Blinding", "class": "OPEN", "state": "OPEN_NOT_SPECIFIED", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Declare who is blinded during acquisition, QC, endpoint extraction and primary analysis." }, { "gate_id": "GATE:NUMERIC_QC", "label": "Numeric assay QC", "class": "OPEN", "state": "OPEN_NUMERIC_THRESHOLDS", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Target-engagement threshold must be numeric and frozen. Viability floor and image-quality thresholds must be numeric and frozen." }, { "gate_id": "GATE:EFFECT_MARGINS", "label": "Effect and equivalence margins", "class": "OPEN", "state": "OPEN_NUMERIC_VALUES_AND_UNITS", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "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." }, { "gate_id": "GATE:ANALYSIS", "label": "Analysis, multiplicity and missingness", "class": "READY", "state": "READY_AS_DRAFT", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "Mixed-effects model with treatment fixed effect and donor/batch/reagent blocking; report reagent-specific estimates. Primary endpoint across the two reagents; secondary endpoints form a separate multiplicity family. Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis." }, { "gate_id": "GATE:STOP_AND_RELEASE", "label": "Stopping and complete release", "class": "READY", "state": "READY_AS_DRAFT", "source": "SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT", "requirement": "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. Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card." }, { "gate_id": "GATE:REGISTRATION", "label": "Immutable registration", "class": "OPEN", "state": "OPEN_NOT_REGISTERED", "source": "/resource/api/v1.1/registered_studies.json", "requirement": "Resolve authority decisions, freeze the plan and deposit an immutable registered Study before execution." }, { "gate_id": "GATE:OUTCOME_SLOT", "label": "Outcome return slot", "class": "OPEN", "state": "OPEN_EMPTY_LEDGER", "source": "/resource/api/v2/outcome_ledger.json", "requirement": "Append every qualifying outcome, including null, toxic, discordant, QC-failed and inconclusive results; never overwrite registration." } ], "design_contract": { "primary_endpoint": "One predeclared functional endpoint, with fusion as the query-selected endpoint", "secondary_endpoints": [ "target engagement", "viability/toxicity", "directional transcriptomic response" ], "primary_estimand": "Between-condition mean difference (or prespecified ratio) in the primary functional endpoint at the frozen time point.", "inferential_unit": "Independent biological replicate or independently generated perturbation unit; cells within one aggregate are not inferential replicates.", "comparator_and_controls": [ "Non-targeting control.", "Positive assay control.", "Mock delivery control when delivery itself can affect phenotype.", "Target-engagement and viability controls." ], "perturbation": "CRISPRi with at least two independent reagents where feasible", "planning_sample_size": "3–6 independent biological replicates per condition and reagent; final powered n remains open", "randomisation_unit": "Independent culture well or biological replicate, not individual cells.", "blocking_factors": [ "Donor/isogenic pair.", "Differentiation batch.", "Plate and reagent identity." ], "statistical_model": "Mixed-effects model with treatment fixed effect and donor/batch/reagent blocking; report reagent-specific estimates.", "multiple_testing_family": "Primary endpoint across the two reagents; secondary endpoints form a separate multiplicity family.", "missing_data_rule": "Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.", "guide_concordance_rule": "Both reagents must agree in direction and neither may fail the engagement/QC gate; discordance is inconclusive.", "donor_replication_rule": "Direction must replicate beyond a single donor or isogenic pair before L4 escalation.", "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." ], "data_release_plan": "Release the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card." }, "unresolved_decisions": [ "Freeze the perturbation direction and its causal, compensatory or accompanying rationale.", "Freeze the primary endpoint scale, minimally important effect and units.", "Freeze the negligible-effect margin and units before interpreting a null result.", "Estimate assay variance and complete the final sample-size calculation.", "Freeze numeric target-engagement, viability and image-quality thresholds.", "Generate the allocation sequence and declare blinding responsibilities.", "Name the experimental authority and create an immutable registration receipt." ], "outcome_slot": { "ledger_path": "/resource/api/v2/outcome_ledger.json", "state": "EMPTY_PENDING_REGISTERED_STUDY_AND_EXPERIMENT", "measured_outcome_count": 0 }, "claim_ceiling": "EXPERIMENT_DESIGN_ONLY", "does_not_imply": [ "that execution is authorized", "that the draft is registered, immutable or powered", "that a DMD perturbation response has been predicted or measured", "that ZNF133 is beneficial, harmful or therapeutically ranked" ], "generated_by": [ "PROCESS:EXPERIMENT_OS_BUILD:V201" ], "is_new_scientific_claim": false, "experiment_plan_sha256": "6b82836351f9f93d6d3f1d3932fa9436baceab58d39195b82efc9d76de139018" }