{ "registry_schema": "nmd-vcell-gse288958-qc-gate/2.0", "dataset_id": "GSE288958", "accession": "GSE288958", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-12T18:15:46+0800", "status": "REFERENCE_CONTEXT_READY_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN", "context_release_ready": true, "context_release_blocking_open_gate_count": 0, "enhancement_open_gate_count": 2, "source_object": { "path": "neuromuscular_virtual_cell/data/external/GSE288958/objects/gse288958_reference_qc_umap_annotated.rds", "sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "class": "Seurat", "cells": 59222, "features": 29242, "opened": true, "identifiers_reconciled": true }, "design": { "samples": 11, "conditions": { "control": 5, "bmd": 3, "dmd": 3 }, "inferential_unit": "independent biopsy/sample; cells remain nested observations", "denominator": { "raw_matrix_cells": 61189, "formal_qc_broad_gate_retained_cells": 59237, "qc_context_gate_retained_cells": 59237, "pilot_rds_cells": 59222, "raw_minus_pilot_cells": 1967, "formal_qc_minus_pilot_cells": 15, "reconciliation_note": "The 61,189 raw-cell inventory, formal matrix-QC denominator and 59,222-cell pilot RDS are preserved as separate denominators; no silent promotion or deletion is performed." } }, "reference_audit": { "audit_id": "GSE288958:REFERENCE-AUDIT:20260909:1", "supersedes_partial_audit_level": "PARTIAL_ANNOTATION_AND_SENSITIVITY_AUDIT", "api_route": "/resource/api/v1.1/gse288958_reference_audit.json", "web_route": "/resource/gse288958-audit/", "independent_doublet_candidates": 1579, "independent_doublet_fraction": 0.026662388977069334, "independent_annotation_resolved_cells": 58912, "independent_annotation_unresolved_cells": 310, "independent_annotation_concordance_fraction_resolved": 0.7588606735469854 }, "matrix_qc": { "status": "COMPLETE_MATRIX_QC_LOW_COUNT_AMBIENT_PROFILE_MARKER_AUDIT", "gate": "nFeature_RNA >= 300 and <= 8000; nCount_RNA >= 500; percent.mt <= 10", "flagged_sample": "Normal_2", "flagged_sample_retained_percent": 61.1548556430446, "sample_summary": { "Normal_1": { "disease": "control", "raw_cells": 9170, "retained_cells": 9166, "retained_percent": 99.9563794983642, "median_nCount_RNA": 4140, "median_nFeature_RNA": 1851, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_2": { "disease": "control", "raw_cells": 4953, "retained_cells": 3029, "retained_percent": 61.1548556430446, "median_nCount_RNA": 582, "median_nFeature_RNA": 403, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_3": { "disease": "control", "raw_cells": 6644, "retained_cells": 6644, "retained_percent": 100, "median_nCount_RNA": 2528, "median_nFeature_RNA": 1145, "median_percent_mt": 0.0391696103966241, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_4": { "disease": "control", "raw_cells": 3775, "retained_cells": 3774, "retained_percent": 99.9735099337748, "median_nCount_RNA": 5197, "median_nFeature_RNA": 2164, "median_percent_mt": 0.0791318109880172, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_5": { "disease": "control", "raw_cells": 4623, "retained_cells": 4621, "retained_percent": 99.956738048886, "median_nCount_RNA": 4463, "median_nFeature_RNA": 1912, "median_percent_mt": 0.0874635568513119, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_1": { "disease": "BMD", "raw_cells": 5521, "retained_cells": 5521, "retained_percent": 100, "median_nCount_RNA": 1332, "median_nFeature_RNA": 859, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_2": { "disease": "BMD", "raw_cells": 8615, "retained_cells": 8613, "retained_percent": 99.9767846778874, "median_nCount_RNA": 2814, "median_nFeature_RNA": 1311, "median_percent_mt": 0.111141983884412, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_3": { "disease": "BMD", "raw_cells": 5341, "retained_cells": 5323, "retained_percent": 99.662984459839, "median_nCount_RNA": 3233, "median_nFeature_RNA": 1629, "median_percent_mt": 0.955667640031856, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_1": { "disease": "DMD", "raw_cells": 3368, "retained_cells": 3368, "retained_percent": 100, "median_nCount_RNA": 1874.5, "median_nFeature_RNA": 1225, "median_percent_mt": 0.0354547612080036, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_2": { "disease": "DMD", "raw_cells": 3063, "retained_cells": 3062, "retained_percent": 99.9673522690173, "median_nCount_RNA": 4742, "median_nFeature_RNA": 2235, "median_percent_mt": 0.146627565982405, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_3": { "disease": "DMD", "raw_cells": 6116, "retained_cells": 6116, "retained_percent": 100, "median_nCount_RNA": 2965.5, "median_nFeature_RNA": 1625, "median_percent_mt": 0.284023684550187, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" } } }, "context_gate": { "stable_modules": [ "FAP_fibroblast:FAP_ECM_fibrosis", "FAP_fibroblast:regeneration_stress", "macrophage_monocyte:macrophage_inflammatory_state", "myonuclei_contractile:oxidative_mito_score", "myonuclei_contractile:regeneration_stress", "satellite_myogenic:regeneration_stress" ], "unstable_modules": [ "macrophage_monocyte:TLR2_NOD2_sensing" ], "candidate_context_only": [ "ADAM10", "CPEB1" ], "normal_2_sensitivity_required": true, "disease_effect_testing_authorized": false, "model_training_labels_allowed": false, "direct_dmd_perturbation_truth": false }, "gates": [ { "gate": "source_object_and_identifiers", "state": "PASS", "evidence": "Seurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled", "closure_required": "None for pilot context; keep the SHA-addressed source object immutable" }, { "gate": "official_processing_metadata", "state": "PASS_PARTIAL_OFFICIAL", "evidence": "GEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples", "closure_required": "Keep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable" }, { "gate": "matrix_qc", "state": "PASS_READ_ONLY", "evidence": "11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity", "closure_required": "Author-exact Cell Ranger/QC reproduction is optional and must remain separate from this route" }, { "gate": "ambient_rna", "state": "OPEN_FORMAL_AMBIENT", "evidence": "Low-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable", "closure_required": "Unfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit" }, { "gate": "doublet", "state": "PASS_INDEPENDENT_SENSITIVITY", "evidence": "Donor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL", "closure_required": "Retain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels" }, { "gate": "independent_annotation", "state": "PASS_INDEPENDENT_AUDIT_BOUNDED", "evidence": "Fixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89%", "closure_required": "Keep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap" }, { "gate": "author_exact_reprocessing", "state": "OPEN_OPTIONAL_AUTHOR_CONFIRMATION", "evidence": "Public software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit", "closure_required": "Required only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse" }, { "gate": "sample_aware_context", "state": "PASS_DESCRIPTIVE_ONLY", "evidence": "6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only", "closure_required": "Use all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels" } ], "operational_boundary": { "sra_route": "DUPLICATE_DOWNLOAD_CLEANED_EXISTING_REFERENCE_RETAINED", "sra_download_required": false, "author_exact_reprocessing": false, "formal_qc_input_preflight": "FORMAL_QC_INPUTS_MANIFEST_MISSING_RETAINED_FOR_AMBIENT_AND_AUTHOR_EXACT_PROMOTION_ONLY", "direct_dmd_candidate_perturbation_truth": "0/21" }, "source_artifacts": { "object_open_audit": { "role": "object_open_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/object_open_audit.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 4234, "sha256": "282a11d6cf69f5e17326b1b7516f785ff8a8327a6b46cac11b49fab2cdfd7833" }, "annotation_audit": { "role": "annotation_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/annotation_audit.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 5708, "sha256": "5df910ea15f644d4a3e104983def2be528f1b1bbade46e0e8b73236c5ec08596" }, "formal_qc_report": { "role": "formal_qc_report", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_report.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 1423, "sha256": "94c0385cf5898ad330d9f41340de5e1f565b00e0189f9e8cab6bf4fc4a4f8d3b" }, "sample_qc": { "role": "sample_qc", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_by_sample.tsv", "state": "FORMAL_QC_AUDIT_TABLE_CHECKSUMMED", "size_bytes": 3046, "sha256": "4493cfc7f8b2bab95d2f46ab80ff672e66cbe78cb3635d8fe36c5b3f442233ca" }, "ambient_estimates": { "role": "ambient_estimates", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_ambient_estimates.tsv", "state": "FORMAL_QC_AUDIT_TABLE_CHECKSUMMED", "size_bytes": 3783, "sha256": "4c722021acad830538a1ed8381564a98c1e5098feaa167a3c4b397654eb4a4fd" }, "qc_context_gate": { "role": "qc_context_gate", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/qc_context_gate/gse288958_qc_context_gate.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 10513, "sha256": "f28edc8e9baa9b0f8914f849b98869964931911d677adfad0bf1bfaef35761e8" }, "formal_qc_preflight": { "role": "formal_qc_preflight", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/formal_qc_input_preflight.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 2080, "sha256": "1b2a08084c9030d76480e282e1992cff773dd00d8c3f121ddf52ca1acbccb785" }, "execution_status": { "role": "execution_status", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_execution_status.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 24920, "sha256": "87a88c6098dff3951471190a23865ed9e43037249b593ecf5c02c2295838e9ef" } }, "claim_boundary": "GSE288958 supports bounded read-only, sample-aware descriptive context with predeclared Normal_2, donor-wise Scrublet and annotation-disagreement sensitivities. Ambient RNA remains unresolved, author-exact Cell Ranger reproduction remains unclaimed, and disease-effect testing, causal claims, model-training labels, therapeutic efficacy and direct DMD perturbation truth remain locked.", "next_action": "Use the reference context with visible Normal_2, Scrublet and annotation-disagreement sensitivities. Seek unfiltered droplets only for ambient-RNA closure and the six exact author artifacts only before an author-exact reprocessing claim.", "markdown": "# GSE288958 formal QC gate\n\n- Status: **REFERENCE_CONTEXT_READY_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN**\n- Checked: 2026-08-12T18:15:46+0800\n- Source object: `ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8`\n- Context-release blocking open gates: **0**\n\n## Current decision\n\nUse the reference context with visible Normal_2, Scrublet and annotation-disagreement sensitivities. Seek unfiltered droplets only for ambient-RNA closure and the six exact author artifacts only before an author-exact reprocessing claim.\n\n## Denominator reconciliation\n\n- Raw matrix inventory: **61,189** cells\n- Formal matrix-QC broad gate: **59,237** cells\n- Pilot RDS: **59,222** cells\n- Raw minus pilot: **1,967** cells\n\nThe 61,189 raw-cell inventory, formal matrix-QC denominator and 59,222-cell pilot RDS are preserved as separate denominators; no silent promotion or deletion is performed.\n\n## Gate table\n\n| Gate | State | Evidence | Closure required |\n|---|---|---|---|\n| source_object_and_identifiers | PASS | Seurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled | None for pilot context; keep the SHA-addressed source object immutable |\n| official_processing_metadata | PASS_PARTIAL_OFFICIAL | GEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples | Keep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable |\n| matrix_qc | PASS_READ_ONLY | 11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity | Author-exact Cell Ranger/QC reproduction is optional and must remain separate from this route |\n| ambient_rna | OPEN_FORMAL_AMBIENT | Low-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable | Unfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit |\n| doublet | PASS_INDEPENDENT_SENSITIVITY | Donor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL | Retain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels |\n| independent_annotation | PASS_INDEPENDENT_AUDIT_BOUNDED | Fixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89% | Keep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap |\n| author_exact_reprocessing | OPEN_OPTIONAL_AUTHOR_CONFIRMATION | Public software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit | Required only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse |\n| sample_aware_context | PASS_DESCRIPTIVE_ONLY | 6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only | Use all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels |\n\n## Independent audits\n\nDonor-wise Scrublet covers **59,222** cells and flags **1,579** candidates. Fixed-marker annotation resolves **58,912** cells, keeps **310** unresolved and reports **75.89%** resolved-label concordance with harmonized inherited labels.\n\n## Allowed use\n\nGSE288958 supports bounded read-only, sample-aware descriptive context with predeclared Normal_2, donor-wise Scrublet and annotation-disagreement sensitivities. Ambient RNA remains unresolved, author-exact Cell Ranger reproduction remains unclaimed, and disease-effect testing, causal claims, model-training labels, therapeutic efficacy and direct DMD perturbation truth remain locked.\n\nDirect DMD candidate perturbation truth remains **0/21**.\n", "tsv": "gate\tstate\tevidence\tclosure_required\nsource_object_and_identifiers\tPASS\tSeurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled\tNone for pilot context; keep the SHA-addressed source object immutable\nofficial_processing_metadata\tPASS_PARTIAL_OFFICIAL\tGEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples\tKeep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable\nmatrix_qc\tPASS_READ_ONLY\t11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity\tAuthor-exact Cell Ranger/QC reproduction is optional and must remain separate from this route\nambient_rna\tOPEN_FORMAL_AMBIENT\tLow-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable\tUnfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit\ndoublet\tPASS_INDEPENDENT_SENSITIVITY\tDonor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL\tRetain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels\nindependent_annotation\tPASS_INDEPENDENT_AUDIT_BOUNDED\tFixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89%\tKeep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap\nauthor_exact_reprocessing\tOPEN_OPTIONAL_AUTHOR_CONFIRMATION\tPublic software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit\tRequired only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse\nsample_aware_context\tPASS_DESCRIPTIVE_ONLY\t6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only\tUse all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels\ndenominator\traw_matrix_cells\t61189\tPreserve raw-versus-pilot denominator gap\ndenominator\tformal_qc_broad_gate_retained_cells\t59237\tKeep formal QC and pilot RDS as distinct objects\ndenominator\tpilot_rds_cells\t59222\tDo not promote pilot denominator silently\n" }