{ "audit_schema": "nmd-vcell-gse288958-reference-audit/2.0", "audit_id": "GSE288958:REFERENCE-AUDIT:20260909:1", "dataset_id": "GSE288958", "accession": "GSE288958", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-09-09", "status": "REFERENCE_CONTEXT_AUDIT_COMPLETE_AMBIENT_AND_AUTHOR_EXACT_REPROCESSING_OPEN", "context_release_ready": true, "context_release_blocking_open_gate_count": 0, "enhancement_open_gate_count": 2, "official_source": { "series_title": "Inhibiting EZH2 complements steroid effects in Duchenne muscular dystrophy", "submission_date": "Feb 06 2025", "last_update_date": "Mar 16 2025", "sample_count": 11, "condition_counts": { "control": 5, "bmd": 3, "dmd": 3 }, "processing_statements": [ "Generated FASTQ files were mapped to human (GRCh38/hg38 pre-mRNA genome) transcriptome references provided by 10x Genomics using Cell Ranger v6.0.0.", "Assembly: GRCh38/hg38", "Supplementary files format and content: tsv, mtx" ], "reported_cell_ranger": "6.0.0", "reported_reference": "human GRCh38/hg38 pre-mRNA genome", "exact_author_command_available": false, "exact_author_parameter_contract_status": "PARTIAL_PROCESSING_CONTRACT_AUTHOR_CONFIRMATION_REQUIRED" }, "denominators": { "geo_matrix_cells": 61189, "broad_gate_retained_cells": 59237, "opened_object_cells": 59222, "opened_object_features": 29242, "raw_minus_opened_object_cells": 1967, "independent_annotation_overlap_cells": 59222, "independent_annotation_resolved_cells": 58912, "independent_annotation_unresolved_cells": 310, "independent_scrublet_cells": 59222, "independent_scrublet_candidates": 1579 }, "sample_unit_contract": { "inferential_unit": "independent biopsy/sample; cells are nested observations", "gsm_count": 11, "biosample_count": 11, "subject_identity_status": "SAMPLE_AND_BIOSAMPLE_PROXY_ONLY_NOT_AUTHOR_CONFIRMED_SUBJECT_IDENTITY", "required_covariates": [ "disease", "biopsy_site", "age" ], "batch_status": "not reported in GEO family SOFT" }, "matrix_qc": { "method": "Read-only per-sample matrix audit", "frozen_gate": "nFeature_RNA >= 300 and <= 8000; nCount_RNA >= 500; percent.mt <= 10", "flagged_sample": "Normal_2", "normal_2_policy": "Retain in the all-sample summary and rerun the descriptive context summary with Normal_2 excluded", "samples": [ { "sample": "Normal_1", "gsm": "GSM8779827", "disease": "control", "raw_matrix_cells": 9170, "broad_gate_retained_cells": 9166, "broad_gate_retained_fraction": 0.999563794983642, "median_counts": 4140, "median_features": 1851, "median_mitochondrial_percent": 0, "normal_2_sensitivity_flag": false }, { "sample": "Normal_2", "gsm": "GSM8779828", "disease": "control", "raw_matrix_cells": 4953, "broad_gate_retained_cells": 3029, "broad_gate_retained_fraction": 0.611548556430446, "median_counts": 582, "median_features": 403, "median_mitochondrial_percent": 0, "normal_2_sensitivity_flag": true }, { "sample": "Normal_3", "gsm": "GSM8779829", "disease": "control", "raw_matrix_cells": 6644, "broad_gate_retained_cells": 6644, "broad_gate_retained_fraction": 1, "median_counts": 2528, "median_features": 1145, "median_mitochondrial_percent": 0.0391696103966241, "normal_2_sensitivity_flag": false }, { "sample": "Normal_4", "gsm": "GSM8779830", "disease": "control", "raw_matrix_cells": 3775, "broad_gate_retained_cells": 3774, "broad_gate_retained_fraction": 0.9997350993377481, "median_counts": 5197, "median_features": 2164, "median_mitochondrial_percent": 0.0791318109880172, "normal_2_sensitivity_flag": false }, { "sample": "Normal_5", "gsm": "GSM8779831", "disease": "control", "raw_matrix_cells": 4623, "broad_gate_retained_cells": 4621, "broad_gate_retained_fraction": 0.99956738048886, "median_counts": 4463, "median_features": 1912, "median_mitochondrial_percent": 0.0874635568513119, "normal_2_sensitivity_flag": false }, { "sample": "BMD_1", "gsm": "GSM8779832", "disease": "BMD", "raw_matrix_cells": 5521, "broad_gate_retained_cells": 5521, "broad_gate_retained_fraction": 1, "median_counts": 1332, "median_features": 859, "median_mitochondrial_percent": 0, "normal_2_sensitivity_flag": false }, { "sample": "BMD_2", "gsm": "GSM8779833", "disease": "BMD", "raw_matrix_cells": 8615, "broad_gate_retained_cells": 8613, "broad_gate_retained_fraction": 0.999767846778874, "median_counts": 2814, "median_features": 1311, "median_mitochondrial_percent": 0.111141983884412, "normal_2_sensitivity_flag": false }, { "sample": "BMD_3", "gsm": "GSM8779834", "disease": "BMD", "raw_matrix_cells": 5341, "broad_gate_retained_cells": 5323, "broad_gate_retained_fraction": 0.99662984459839, "median_counts": 3233, "median_features": 1629, "median_mitochondrial_percent": 0.955667640031856, "normal_2_sensitivity_flag": false }, { "sample": "DMD_1", "gsm": "GSM8779835", "disease": "DMD", "raw_matrix_cells": 3368, "broad_gate_retained_cells": 3368, "broad_gate_retained_fraction": 1, "median_counts": 1874.5, "median_features": 1225, "median_mitochondrial_percent": 0.0354547612080036, "normal_2_sensitivity_flag": false }, { "sample": "DMD_2", "gsm": "GSM8779836", "disease": "DMD", "raw_matrix_cells": 3063, "broad_gate_retained_cells": 3062, "broad_gate_retained_fraction": 0.999673522690173, "median_counts": 4742, "median_features": 2235, "median_mitochondrial_percent": 0.146627565982405, "normal_2_sensitivity_flag": false }, { "sample": "DMD_3", "gsm": "GSM8779837", "disease": "DMD", "raw_matrix_cells": 6116, "broad_gate_retained_cells": 6116, "broad_gate_retained_fraction": 1, "median_counts": 2965.5, "median_features": 1625, "median_mitochondrial_percent": 0.284023684550187, "normal_2_sensitivity_flag": false } ] }, "independent_doublet_audit": { "method": "scanpy.pp.scrublet", "software": "Scanpy 1.12.1", "per_sample_run": true, "parameters": { "expected_doublet_rate": 0.05, "sim_doublet_ratio": 2, "n_prin_comps": 30, "random_state": 20260720 }, "object_cells": 59222, "exact_object_cell_key_set_match": true, "predicted_doublets": 1579, "predicted_doublet_fraction": 0.026662388977069334, "isolated_rerun_status": "IDENTICAL", "baseline_object_modified": false, "samples": [ { "sample": "Normal_1", "object_cells": 9165, "expected_doublet_rate": 0.05, "predicted_doublets": 509, "predicted_doublet_fraction": 0.05553737043098745, "median_doublet_score": 0.041723979825768004, "automatic_threshold": 0.18989376533726093 }, { "sample": "Normal_2", "object_cells": 3020, "expected_doublet_rate": 0.05, "predicted_doublets": 40, "predicted_doublet_fraction": 0.013245033112582781, "median_doublet_score": 0.06423982869379015, "automatic_threshold": 0.3141136122296999 }, { "sample": "Normal_3", "object_cells": 6642, "expected_doublet_rate": 0.05, "predicted_doublets": 159, "predicted_doublet_fraction": 0.023938572719060525, "median_doublet_score": 0.022984028048305412, "automatic_threshold": 0.25189153289385413 }, { "sample": "Normal_4", "object_cells": 3774, "expected_doublet_rate": 0.05, "predicted_doublets": 82, "predicted_doublet_fraction": 0.02172760996290408, "median_doublet_score": 0.04134548002803085, "automatic_threshold": 0.2642399407679737 }, { "sample": "Normal_5", "object_cells": 4621, "expected_doublet_rate": 0.05, "predicted_doublets": 72, "predicted_doublet_fraction": 0.015581043064271802, "median_doublet_score": 0.0309278350515464, "automatic_threshold": 0.256311447040073 }, { "sample": "BMD_1", "object_cells": 5518, "expected_doublet_rate": 0.05, "predicted_doublets": 121, "predicted_doublet_fraction": 0.02192823486770569, "median_doublet_score": 0.020458265139116208, "automatic_threshold": 0.22950108817989712 }, { "sample": "BMD_2", "object_cells": 8613, "expected_doublet_rate": 0.05, "predicted_doublets": 319, "predicted_doublet_fraction": 0.037037037037037035, "median_doublet_score": 0.06597671410090555, "automatic_threshold": 0.25427030256911154 }, { "sample": "BMD_3", "object_cells": 5323, "expected_doublet_rate": 0.05, "predicted_doublets": 111, "predicted_doublet_fraction": 0.02085290249859102, "median_doublet_score": 0.0655737704918033, "automatic_threshold": 0.2870680876336677 }, { "sample": "DMD_1", "object_cells": 3368, "expected_doublet_rate": 0.05, "predicted_doublets": 29, "predicted_doublet_fraction": 0.0086104513064133, "median_doublet_score": 0.02620850320326151, "automatic_threshold": 0.27550488488995173 }, { "sample": "DMD_2", "object_cells": 3062, "expected_doublet_rate": 0.05, "predicted_doublets": 7, "predicted_doublet_fraction": 0.0022860875244937948, "median_doublet_score": 0.023415191319246145, "automatic_threshold": 0.458991055003282 }, { "sample": "DMD_3", "object_cells": 6116, "expected_doublet_rate": 0.05, "predicted_doublets": 130, "predicted_doublet_fraction": 0.021255722694571617, "median_doublet_score": 0.020015396458814474, "automatic_threshold": 0.23791155368239847 } ], "interpretation": "Independent algorithmic doublet sensitivity is complete and reproducible. Calls remain a sensitivity layer rather than authoritative deletions." }, "independent_annotation_audit": { "method": "Fixed marker-panel fraction of total counts; argmax label; unresolved when all panel scores are zero", "inherited_annotation_role": "Inherited coarse labels from the checksum-matched opened Seurat object", "independent_annotation_role": "Analyst-generated rule-based marker audit on the released count matrices", "marker_panels": { "myonuclei": [ "MYH1", "MYH2", "MYH3", "MYH4", "MYL1", "ACTA1", "DES", "TTN" ], "satellite": [ "PAX7", "MYF5", "MYOD1", "VCAM1", "CD34", "NOTCH3" ], "fibroblast": [ "COL1A1", "COL1A2", "DCN", "LUM", "COL3A1", "PDGFRA" ], "endothelial": [ "PECAM1", "VWF", "EMCN", "KDR", "RAMP2", "ENG" ], "pericyte": [ "RGS5", "CSPG4", "MCAM", "COL4A1", "COL4A2" ], "macrophage": [ "LST1", "TYROBP", "FCER1G", "CTSS", "C1QA", "C1QB" ], "t_nk": [ "CD3D", "CD3E", "TRBC1", "NKG7", "GNLY" ] }, "object_cells": 59222, "exact_object_cell_overlap": 59222, "resolved_cells": 58912, "unresolved_cells": 310, "unresolved_fraction": 0.005234541217790686, "concordant_cells": 44706, "concordance_fraction_resolved": 0.7588606735469854, "inherited_internal_marker_argmax_agreement": 0.8106, "unresolved_policy": "Keep unresolved cells as unresolved; do not impute or overwrite inherited labels. Preserve every disagreement in the confusion table.", "known_panel_gap": "No independent B/plasma marker panel is present in the frozen audit method; B_plasma concordance therefore cannot be established by this audit.", "by_inherited_label": [ { "inherited_object_label": "B_plasma", "expected_harmonized_label": "b_plasma", "object_cells": 577, "independently_resolved_cells": 542, "unresolved_cells": 35, "concordant_cells": 0, "concordance_fraction_resolved": 0, "most_common_independent_label": "myonuclei", "most_common_independent_label_cells": 435 }, { "inherited_object_label": "endothelial", "expected_harmonized_label": "endothelial", "object_cells": 5016, "independently_resolved_cells": 4994, "unresolved_cells": 22, "concordant_cells": 3336, "concordance_fraction_resolved": 0.6680016019223067, "most_common_independent_label": "endothelial", "most_common_independent_label_cells": 3336 }, { "inherited_object_label": "FAP_fibroblast", "expected_harmonized_label": "fibroblast", "object_cells": 9294, "independently_resolved_cells": 9282, "unresolved_cells": 12, "concordant_cells": 6841, "concordance_fraction_resolved": 0.7370178840767077, "most_common_independent_label": "fibroblast", "most_common_independent_label_cells": 6841 }, { "inherited_object_label": "macrophage_monocyte", "expected_harmonized_label": "macrophage", "object_cells": 4332, "independently_resolved_cells": 4257, "unresolved_cells": 75, "concordant_cells": 896, "concordance_fraction_resolved": 0.21047686163965235, "most_common_independent_label": "myonuclei", "most_common_independent_label_cells": 2803 }, { "inherited_object_label": "myonuclei_contractile", "expected_harmonized_label": "myonuclei", "object_cells": 30395, "independently_resolved_cells": 30393, "unresolved_cells": 2, "concordant_cells": 30391, "concordance_fraction_resolved": 0.9999341953739348, "most_common_independent_label": "myonuclei", "most_common_independent_label_cells": 30391 }, { "inherited_object_label": "pericyte_smooth", "expected_harmonized_label": "pericyte", "object_cells": 1822, "independently_resolved_cells": 1814, "unresolved_cells": 8, "concordant_cells": 844, "concordance_fraction_resolved": 0.4652701212789416, "most_common_independent_label": "pericyte", "most_common_independent_label_cells": 844 }, { "inherited_object_label": "satellite_myogenic", "expected_harmonized_label": "satellite", "object_cells": 5704, "independently_resolved_cells": 5647, "unresolved_cells": 57, "concordant_cells": 2194, "concordance_fraction_resolved": 0.3885248804675049, "most_common_independent_label": "myonuclei", "most_common_independent_label_cells": 2506 }, { "inherited_object_label": "T_NK", "expected_harmonized_label": "t_nk", "object_cells": 2082, "independently_resolved_cells": 1983, "unresolved_cells": 99, "concordant_cells": 204, "concordance_fraction_resolved": 0.10287443267776097, "most_common_independent_label": "myonuclei", "most_common_independent_label_cells": 1592 } ], "confusion_matrix": [ { "inherited_object_label": "B_plasma", "independent_marker_label": "myonuclei", "cells": 435 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "fibroblast", "cells": 38 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "macrophage", "cells": 38 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "unresolved", "cells": 35 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "endothelial", "cells": 20 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "pericyte", "cells": 7 }, { "inherited_object_label": "B_plasma", "independent_marker_label": "satellite", "cells": 4 }, { "inherited_object_label": "endothelial", "independent_marker_label": "endothelial", "cells": 3336 }, { "inherited_object_label": "endothelial", "independent_marker_label": "myonuclei", "cells": 999 }, { "inherited_object_label": "endothelial", "independent_marker_label": "pericyte", "cells": 561 }, { "inherited_object_label": "endothelial", "independent_marker_label": "fibroblast", "cells": 68 }, { "inherited_object_label": "endothelial", "independent_marker_label": "satellite", "cells": 26 }, { "inherited_object_label": "endothelial", "independent_marker_label": "unresolved", "cells": 22 }, { "inherited_object_label": "endothelial", "independent_marker_label": "macrophage", "cells": 4 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "fibroblast", "cells": 6841 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "myonuclei", "cells": 1221 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "pericyte", "cells": 1180 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "satellite", "cells": 22 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "endothelial", "cells": 17 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "unresolved", "cells": 12 }, { "inherited_object_label": "FAP_fibroblast", "independent_marker_label": "macrophage", "cells": 1 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "myonuclei", "cells": 2803 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "macrophage", "cells": 896 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "endothelial", "cells": 306 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "fibroblast", "cells": 203 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "unresolved", "cells": 75 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "pericyte", "cells": 27 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "satellite", "cells": 20 }, { "inherited_object_label": "macrophage_monocyte", "independent_marker_label": "t_nk", "cells": 2 }, { "inherited_object_label": "myonuclei_contractile", "independent_marker_label": "myonuclei", "cells": 30391 }, { "inherited_object_label": "myonuclei_contractile", "independent_marker_label": "unresolved", "cells": 2 }, { "inherited_object_label": "myonuclei_contractile", "independent_marker_label": "fibroblast", "cells": 1 }, { "inherited_object_label": "myonuclei_contractile", "independent_marker_label": "endothelial", "cells": 1 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "pericyte", "cells": 844 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "myonuclei", "cells": 666 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "fibroblast", "cells": 138 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "satellite", "cells": 132 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "endothelial", "cells": 33 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "unresolved", "cells": 8 }, { "inherited_object_label": "pericyte_smooth", "independent_marker_label": "macrophage", "cells": 1 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "myonuclei", "cells": 2506 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "satellite", "cells": 2194 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "fibroblast", "cells": 610 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "pericyte", "cells": 319 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "unresolved", "cells": 57 }, { "inherited_object_label": "satellite_myogenic", "independent_marker_label": "endothelial", "cells": 18 }, { "inherited_object_label": "T_NK", "independent_marker_label": "myonuclei", "cells": 1592 }, { "inherited_object_label": "T_NK", "independent_marker_label": "t_nk", "cells": 204 }, { "inherited_object_label": "T_NK", "independent_marker_label": "fibroblast", "cells": 111 }, { "inherited_object_label": "T_NK", "independent_marker_label": "unresolved", "cells": 99 }, { "inherited_object_label": "T_NK", "independent_marker_label": "endothelial", "cells": 30 }, { "inherited_object_label": "T_NK", "independent_marker_label": "macrophage", "cells": 25 }, { "inherited_object_label": "T_NK", "independent_marker_label": "pericyte", "cells": 14 }, { "inherited_object_label": "T_NK", "independent_marker_label": "satellite", "cells": 7 } ] }, "gates": [ { "gate": "official_source_matrix_integrity", "state": "PASS", "blocks_context_release": true, "evidence": "GEO archive 32 members plus the separate BMD_1 feature table reconcile 11 matrices and 61,189 barcodes", "remaining_boundary": "Released matrices contain selected barcodes; they are not unfiltered droplet matrices" }, { "gate": "official_processing_metadata", "state": "PASS_PARTIAL_OFFICIAL", "blocks_context_release": true, "evidence": "GEO SOFT reports Cell Ranger 6.0.0 and a GRCh38/hg38 pre-mRNA reference for all 11 samples", "remaining_boundary": "Exact author command, read structure, whitelist, reference checksum, sample sheet and FASTQ aggregation manifest remain unavailable" }, { "gate": "object_and_identifier_reconciliation", "state": "PASS", "blocks_context_release": true, "evidence": "Seurat opened read-only; 59,222 cells × 29,242 features; cell, sample and feature identities reconcile", "remaining_boundary": "Preserve the source object hash and the 1,967-cell raw-to-object denominator gap" }, { "gate": "sample_unit_contract", "state": "PASS_SAMPLE_BIOPSY_LEVEL", "blocks_context_release": true, "evidence": "11 GSM accessions map one-to-one to 11 BioSample accessions and named biopsy/sample units", "remaining_boundary": "Subject-level identifiers are not published; use biopsy/sample as the independent unit and keep site, age and disease explicit" }, { "gate": "read_only_matrix_qc", "state": "PASS_WITH_SENSITIVITY", "blocks_context_release": true, "evidence": "59,237 of 61,189 matrix cells pass the frozen broad gate; Normal_2 is retained and predeclared for exclusion sensitivity", "remaining_boundary": "The broad gate is an independent audit and does not claim author-exact filtering" }, { "gate": "independent_doublet_audit", "state": "PASS_INDEPENDENT_SENSITIVITY", "blocks_context_release": true, "evidence": "Donor-wise Scanpy Scrublet maps 59,222/59,222 object cells and flags 1,579 (2.67%); isolated rerun is byte-identical", "remaining_boundary": "Algorithmic candidates remain a sensitivity layer; the baseline object is not overwritten and calls are not author labels" }, { "gate": "independent_annotation_audit", "state": "PASS_INDEPENDENT_AUDIT_BOUNDED", "blocks_context_release": true, "evidence": "Independent fixed-marker scoring covers 59,222/59,222 object cells; 58,912 resolve and 44,706 agree with harmonized inherited labels (75.89%)", "remaining_boundary": "Keep 310 unresolved cells unresolved; B/plasma lacks an independent marker panel, and disagreements remain visible rather than being overwritten" }, { "gate": "ambient_rna", "state": "OPEN_UNFILTERED_DROPLETS_UNAVAILABLE", "blocks_context_release": false, "evidence": "A low-count expression profile is available only as a proxy; released matrices do not identify empty droplets", "remaining_boundary": "Requires raw_feature_bc_matrix/unfiltered droplets or author contamination estimates for emptyDrops/SoupX closure" }, { "gate": "author_exact_reprocessing", "state": "OPEN_OPTIONAL_AUTHOR_CONFIRMATION", "blocks_context_release": false, "evidence": "The public processing version and genome family are known, while all six exact execution artifacts remain absent after a provenance-aware local audit", "remaining_boundary": "Required only before claiming author-exact Cell Ranger reproduction; it is not required for the bounded read-only context release" }, { "gate": "disease_effect_and_model_labels", "state": "LOCKED_NOT_AUTHORIZED", "blocks_context_release": false, "evidence": "No disease-effect p-value, causal contrast, candidate-conditioned DMD outcome or training label is created by this audit", "remaining_boundary": "A separate donor/sample-aware statistical contract and outcome-specific validation are required" } ], "open_enhancement_gates": [ "ambient_rna", "author_exact_reprocessing" ], "source_artifacts": { "family_soft": { "role": "family_soft", "path": "neuromuscular_virtual_cell/data/external/GSE288958/raw/GSE288958_family.soft.gz", "size_bytes": 3433, "sha256": "7a833abb4227d62d54c323fc16c1bc0eded7f4c8226326348b4d81e919184e3e", "state": "SOURCE_CHECKSUMMED" }, "raw_inventory": { "role": "raw_inventory", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/GSE288958_raw_cell_inventory_manifest.json", "size_bytes": 7254, "sha256": "91b872d11e4a494065949f99118951ea2a433e0f67f4e1d37b0909de5b188f63", "state": "SOURCE_CHECKSUMMED" }, "object_open_audit": { "role": "object_open_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/object_open_audit.json", "size_bytes": 4234, "sha256": "282a11d6cf69f5e17326b1b7516f785ff8a8327a6b46cac11b49fab2cdfd7833", "state": "SOURCE_CHECKSUMMED" }, "annotation_provenance": { "role": "annotation_provenance", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/candidate_annotation_provenance.json", "size_bytes": 4223, "sha256": "4ebcb2e7ceacdeea841ed0940840730449fdcbdf0a5c1cfe5a6597cd6e791bb5", "state": "SOURCE_CHECKSUMMED" }, "inherited_annotations": { "role": "inherited_annotations", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/cell_annotations.csv", "size_bytes": 18792250, "sha256": "f9f38dca26ae43d82b628c37f4d991fdb9fe6269133369b5e3ecfb767f892ca6", "state": "SOURCE_CHECKSUMMED" }, "formal_report": { "role": "formal_report", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_report.json", "size_bytes": 1423, "sha256": "94c0385cf5898ad330d9f41340de5e1f565b00e0189f9e8cab6bf4fc4a4f8d3b", "state": "SOURCE_CHECKSUMMED" }, "formal_cell_qc": { "role": "formal_cell_qc", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_cell_qc.tsv.gz", "size_bytes": 1944465, "sha256": "39150bff12bf51f02d6b6fea3d9b4d1fc47b1cee6fc385a0a911aaa846dc978c", "state": "SOURCE_CHECKSUMMED" }, "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", "size_bytes": 3046, "sha256": "4493cfc7f8b2bab95d2f46ab80ff672e66cbe78cb3635d8fe36c5b3f442233ca", "state": "SOURCE_CHECKSUMMED" }, "parameter_audit": { "role": "parameter_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_parameter_recovery_audit.json", "size_bytes": 12540, "sha256": "3baaf3b858e9831cb53b678faffd2dcaa3582bca02684614f553ca6b1e5f43bb", "state": "SOURCE_CHECKSUMMED" }, "processing_contract": { "role": "processing_contract", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_processing_contract.json", "size_bytes": 32794, "sha256": "e90a5f3dccb2e46969e2d30f183181244d9094a06efc56ed8d67ae803f152a7f", "state": "SOURCE_CHECKSUMMED" }, "independent_annotation_method": { "role": "independent_annotation_method", "path": "neuromuscular_virtual_cell/scripts/run_gse288958_existing_reference_qc_remote.R", "size_bytes": 11375, "sha256": "7541cb15be8491418d253a4fcef1b239178db30ad44091f315c131154f2f14c8", "state": "SOURCE_CHECKSUMMED" }, "scrublet_calls": { "role": "scrublet_calls", "path": "24.GFOD2/results/qc/m01b/gse288958_scrublet_calls_by_cell.tsv", "size_bytes": 3553565, "sha256": "f723359260a6f08ded3552e6b8360230eec64ca3d0cda7de986d8cdc8b5f00cc", "state": "SOURCE_CHECKSUMMED" }, "scrublet_summary": { "role": "scrublet_summary", "path": "24.GFOD2/results/qc/m01b/gse288958_scrublet_summary_by_donor.tsv", "size_bytes": 1251, "sha256": "d41b238eec7540c57636e4d5330829b6587886b47d5d79c14775c808806dc7a4", "state": "SOURCE_CHECKSUMMED" }, "scrublet_plan": { "role": "scrublet_plan", "path": "24.GFOD2/configs/gse288958_m01b_scrublet_plan_v1.yaml", "size_bytes": 959, "sha256": "e037a74d0ad931ea58b2bb0691abb681ec95329a39bdfe4b4614500fb36051e2", "state": "SOURCE_CHECKSUMMED" }, "scrublet_rerun": { "role": "scrublet_rerun", "path": "24.GFOD2/results/qc/m01b/gse288958_scrublet_isolated_rerun_status.txt", "size_bytes": 10, "sha256": "1e00073b48fe3b36fc839da3b74b515bbecc9def677e059553835bb86bde8c55", "state": "SOURCE_CHECKSUMMED" }, "official_raw_archive": { "role": "official_raw_archive", "path": "neuromuscular_virtual_cell/data/external/GSE288958/raw/GSE288958_RAW.tar", "size_bytes": 359823360, "sha256": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "state": "OFFICIAL_GEO_ARCHIVE_HASH_AND_GZIP_STREAMS_VALIDATED" }, "authoritative_reference_rds": { "role": "authoritative_reference_rds", "path": "neuromuscular_virtual_cell/data/external/GSE288958/objects/gse288958_reference_qc_umap_annotated.rds", "size_bytes": 1847703081, "sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "state": "OPENED_READ_ONLY_AND_IDENTIFIER_RECONCILED" } }, "allowed_use": [ "Read-only sample-aware descriptive DMD/BMD/control muscle context", "All-sample and predeclared Normal_2-excluded sensitivity summaries", "Inherited-label analyses accompanied by the independent annotation disagreement audit", "Independent Scrublet exclusion sensitivity without overwriting the baseline object" ], "prohibited_use": [ "Candidate-conditioned DMD perturbation outcome or training label", "Disease-effect p-value or causal claim from nested cells", "Therapeutic efficacy or clinical recommendation", "Author-exact Cell Ranger reproduction", "Formal ambient-RNA clearance" ], "claim_boundary": "The checksum-matched GSE288958 reference is ready for bounded, read-only, sample-aware descriptive context. Independent doublet and annotation audits are complete as sensitivity and disagreement layers. Ambient RNA remains unresolved because unfiltered droplets are unavailable, author-exact reprocessing remains unclaimed, and no disease-effect, causal, model-training, therapeutic or direct candidate-level DMD perturbation conclusion is authorized.", "next_action": "Use the released reference context with Normal_2 and Scrublet sensitivities plus visible annotation disagreement. Seek unfiltered droplets or author contamination estimates only to close ambient RNA, and seek the six exact author artifacts only before an author-exact reprocessing claim.", "gate_tsv": "gate\tstate\tblocks_context_release\tevidence\tremaining_boundary\nofficial_source_matrix_integrity\tPASS\ttrue\tGEO archive 32 members plus the separate BMD_1 feature table reconcile 11 matrices and 61,189 barcodes\tReleased matrices contain selected barcodes; they are not unfiltered droplet matrices\nofficial_processing_metadata\tPASS_PARTIAL_OFFICIAL\ttrue\tGEO SOFT reports Cell Ranger 6.0.0 and a GRCh38/hg38 pre-mRNA reference for all 11 samples\tExact author command, read structure, whitelist, reference checksum, sample sheet and FASTQ aggregation manifest remain unavailable\nobject_and_identifier_reconciliation\tPASS\ttrue\tSeurat opened read-only; 59,222 cells × 29,242 features; cell, sample and feature identities reconcile\tPreserve the source object hash and the 1,967-cell raw-to-object denominator gap\nsample_unit_contract\tPASS_SAMPLE_BIOPSY_LEVEL\ttrue\t11 GSM accessions map one-to-one to 11 BioSample accessions and named biopsy/sample units\tSubject-level identifiers are not published; use biopsy/sample as the independent unit and keep site, age and disease explicit\nread_only_matrix_qc\tPASS_WITH_SENSITIVITY\ttrue\t59,237 of 61,189 matrix cells pass the frozen broad gate; Normal_2 is retained and predeclared for exclusion sensitivity\tThe broad gate is an independent audit and does not claim author-exact filtering\nindependent_doublet_audit\tPASS_INDEPENDENT_SENSITIVITY\ttrue\tDonor-wise Scanpy Scrublet maps 59,222/59,222 object cells and flags 1,579 (2.67%); isolated rerun is byte-identical\tAlgorithmic candidates remain a sensitivity layer; the baseline object is not overwritten and calls are not author labels\nindependent_annotation_audit\tPASS_INDEPENDENT_AUDIT_BOUNDED\ttrue\tIndependent fixed-marker scoring covers 59,222/59,222 object cells; 58,912 resolve and 44,706 agree with harmonized inherited labels (75.89%)\tKeep 310 unresolved cells unresolved; B/plasma lacks an independent marker panel, and disagreements remain visible rather than being overwritten\nambient_rna\tOPEN_UNFILTERED_DROPLETS_UNAVAILABLE\tfalse\tA low-count expression profile is available only as a proxy; released matrices do not identify empty droplets\tRequires raw_feature_bc_matrix/unfiltered droplets or author contamination estimates for emptyDrops/SoupX closure\nauthor_exact_reprocessing\tOPEN_OPTIONAL_AUTHOR_CONFIRMATION\tfalse\tThe public processing version and genome family are known, while all six exact execution artifacts remain absent after a provenance-aware local audit\tRequired only before claiming author-exact Cell Ranger reproduction; it is not required for the bounded read-only context release\ndisease_effect_and_model_labels\tLOCKED_NOT_AUTHORIZED\tfalse\tNo disease-effect p-value, causal contrast, candidate-conditioned DMD outcome or training label is created by this audit\tA separate donor/sample-aware statistical contract and outcome-specific validation are required\n", "annotation_summary_tsv": "inherited_object_label\texpected_harmonized_label\tobject_cells\tindependently_resolved_cells\tunresolved_cells\tconcordant_cells\tconcordance_fraction_resolved\tmost_common_independent_label\tmost_common_independent_label_cells\nB_plasma\tb_plasma\t577\t542\t35\t0\t0\tmyonuclei\t435\nendothelial\tendothelial\t5016\t4994\t22\t3336\t0.6680016019223067\tendothelial\t3336\nFAP_fibroblast\tfibroblast\t9294\t9282\t12\t6841\t0.7370178840767077\tfibroblast\t6841\nmacrophage_monocyte\tmacrophage\t4332\t4257\t75\t896\t0.21047686163965235\tmyonuclei\t2803\nmyonuclei_contractile\tmyonuclei\t30395\t30393\t2\t30391\t0.9999341953739348\tmyonuclei\t30391\npericyte_smooth\tpericyte\t1822\t1814\t8\t844\t0.4652701212789416\tpericyte\t844\nsatellite_myogenic\tsatellite\t5704\t5647\t57\t2194\t0.3885248804675049\tmyonuclei\t2506\nT_NK\tt_nk\t2082\t1983\t99\t204\t0.10287443267776097\tmyonuclei\t1592\n", "annotation_confusion_tsv": "inherited_object_label\tindependent_marker_label\tcells\nB_plasma\tmyonuclei\t435\nB_plasma\tfibroblast\t38\nB_plasma\tmacrophage\t38\nB_plasma\tunresolved\t35\nB_plasma\tendothelial\t20\nB_plasma\tpericyte\t7\nB_plasma\tsatellite\t4\nendothelial\tendothelial\t3336\nendothelial\tmyonuclei\t999\nendothelial\tpericyte\t561\nendothelial\tfibroblast\t68\nendothelial\tsatellite\t26\nendothelial\tunresolved\t22\nendothelial\tmacrophage\t4\nFAP_fibroblast\tfibroblast\t6841\nFAP_fibroblast\tmyonuclei\t1221\nFAP_fibroblast\tpericyte\t1180\nFAP_fibroblast\tsatellite\t22\nFAP_fibroblast\tendothelial\t17\nFAP_fibroblast\tunresolved\t12\nFAP_fibroblast\tmacrophage\t1\nmacrophage_monocyte\tmyonuclei\t2803\nmacrophage_monocyte\tmacrophage\t896\nmacrophage_monocyte\tendothelial\t306\nmacrophage_monocyte\tfibroblast\t203\nmacrophage_monocyte\tunresolved\t75\nmacrophage_monocyte\tpericyte\t27\nmacrophage_monocyte\tsatellite\t20\nmacrophage_monocyte\tt_nk\t2\nmyonuclei_contractile\tmyonuclei\t30391\nmyonuclei_contractile\tunresolved\t2\nmyonuclei_contractile\tfibroblast\t1\nmyonuclei_contractile\tendothelial\t1\npericyte_smooth\tpericyte\t844\npericyte_smooth\tmyonuclei\t666\npericyte_smooth\tfibroblast\t138\npericyte_smooth\tsatellite\t132\npericyte_smooth\tendothelial\t33\npericyte_smooth\tunresolved\t8\npericyte_smooth\tmacrophage\t1\nsatellite_myogenic\tmyonuclei\t2506\nsatellite_myogenic\tsatellite\t2194\nsatellite_myogenic\tfibroblast\t610\nsatellite_myogenic\tpericyte\t319\nsatellite_myogenic\tunresolved\t57\nsatellite_myogenic\tendothelial\t18\nT_NK\tmyonuclei\t1592\nT_NK\tt_nk\t204\nT_NK\tfibroblast\t111\nT_NK\tunresolved\t99\nT_NK\tendothelial\t30\nT_NK\tmacrophage\t25\nT_NK\tpericyte\t14\nT_NK\tsatellite\t7\n", "doublet_by_sample_tsv": "sample\tobject_cells\texpected_doublet_rate\tpredicted_doublets\tpredicted_doublet_fraction\tmedian_doublet_score\tautomatic_threshold\nNormal_1\t9165\t0.05\t509\t0.05553737043098745\t0.041723979825768004\t0.18989376533726093\nNormal_2\t3020\t0.05\t40\t0.013245033112582781\t0.06423982869379015\t0.3141136122296999\nNormal_3\t6642\t0.05\t159\t0.023938572719060525\t0.022984028048305412\t0.25189153289385413\nNormal_4\t3774\t0.05\t82\t0.02172760996290408\t0.04134548002803085\t0.2642399407679737\nNormal_5\t4621\t0.05\t72\t0.015581043064271802\t0.0309278350515464\t0.256311447040073\nBMD_1\t5518\t0.05\t121\t0.02192823486770569\t0.020458265139116208\t0.22950108817989712\nBMD_2\t8613\t0.05\t319\t0.037037037037037035\t0.06597671410090555\t0.25427030256911154\nBMD_3\t5323\t0.05\t111\t0.02085290249859102\t0.0655737704918033\t0.2870680876336677\nDMD_1\t3368\t0.05\t29\t0.0086104513064133\t0.02620850320326151\t0.27550488488995173\nDMD_2\t3062\t0.05\t7\t0.0022860875244937948\t0.023415191319246145\t0.458991055003282\nDMD_3\t6116\t0.05\t130\t0.021255722694571617\t0.020015396458814474\t0.23791155368239847\n", "sample_qc_tsv": "sample\tgsm\tdisease\traw_matrix_cells\tbroad_gate_retained_cells\tbroad_gate_retained_fraction\tmedian_counts\tmedian_features\tmedian_mitochondrial_percent\tnormal_2_sensitivity_flag\nNormal_1\tGSM8779827\tcontrol\t9170\t9166\t0.999563794983642\t4140\t1851\t0\tfalse\nNormal_2\tGSM8779828\tcontrol\t4953\t3029\t0.611548556430446\t582\t403\t0\ttrue\nNormal_3\tGSM8779829\tcontrol\t6644\t6644\t1\t2528\t1145\t0.0391696103966241\tfalse\nNormal_4\tGSM8779830\tcontrol\t3775\t3774\t0.9997350993377481\t5197\t2164\t0.0791318109880172\tfalse\nNormal_5\tGSM8779831\tcontrol\t4623\t4621\t0.99956738048886\t4463\t1912\t0.0874635568513119\tfalse\nBMD_1\tGSM8779832\tBMD\t5521\t5521\t1\t1332\t859\t0\tfalse\nBMD_2\tGSM8779833\tBMD\t8615\t8613\t0.999767846778874\t2814\t1311\t0.111141983884412\tfalse\nBMD_3\tGSM8779834\tBMD\t5341\t5323\t0.99662984459839\t3233\t1629\t0.955667640031856\tfalse\nDMD_1\tGSM8779835\tDMD\t3368\t3368\t1\t1874.5\t1225\t0.0354547612080036\tfalse\nDMD_2\tGSM8779836\tDMD\t3063\t3062\t0.999673522690173\t4742\t2235\t0.146627565982405\tfalse\nDMD_3\tGSM8779837\tDMD\t6116\t6116\t1\t2965.5\t1625\t0.284023684550187\tfalse\n", "markdown": "# GSE288958 reference QC and independent-audit closure\n\n- Status: **REFERENCE_CONTEXT_AUDIT_COMPLETE_AMBIENT_AND_AUTHOR_EXACT_REPROCESSING_OPEN**\n- Checked: 2026-09-09\n- Context release blocking open gates: **0**\n- Enhancement gates still open: **ambient_rna, author_exact_reprocessing**\n\n## Source and denominators\n\nGEO reports Cell Ranger **6.0.0** with a **GRCh38/hg38 pre-mRNA** reference. The released matrices contain **61,189** selected barcodes across 11 samples. The opened Seurat object contains **59,222** cells and **29,242** features; the **1,967**-cell gap remains explicit.\n\n## Independent doublet audit\n\nDonor-wise Scanpy Scrublet covers **59,222/59,222** object cells and flags **1,579 (2.67%)** candidates. The isolated rerun is **IDENTICAL**. Calls remain a sensitivity layer and do not overwrite the baseline object.\n\n## Independent annotation audit\n\nFixed marker panels cover **59,222/59,222** object cells. **58,912** receive an independent marker label, **310** remain unresolved, and **44,706** resolved cells agree with harmonized inherited labels (**75.89%**). Disagreements remain public; the audit does not promote either label source to biological truth.\n\n## Remaining boundaries\n\n- Ambient RNA remains open because the released matrices do not identify empty droplets.\n- The exact author command, read structure, whitelist, reference checksum, sample sheet and FASTQ aggregation manifest remain unavailable.\n- Subject identity is represented by one GSM/BioSample biopsy unit; cells remain nested observations.\n- Disease-effect testing and direct candidate-level DMD perturbation truth remain locked.\n\n## Claim boundary\n\nThe checksum-matched GSE288958 reference is ready for bounded, read-only, sample-aware descriptive context. Independent doublet and annotation audits are complete as sensitivity and disagreement layers. Ambient RNA remains unresolved because unfiltered droplets are unavailable, author-exact reprocessing remains unclaimed, and no disease-effect, causal, model-training, therapeutic or direct candidate-level DMD perturbation conclusion is authorized.\n" }