{ "registry_schema": "nmd-vcell-data-opportunity-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "record_count": 13, "records": [ { "opportunity_id": "DATA-AUTHOR-MISSING-FEATURE-METADATA", "name": "Author-missing feature and metadata files", "provider": "Source authors / existing DMD perturbation study", "data_class": "DECISION_CRITICAL_SOURCE_RECOVERY", "scale": "Unknown until files are obtained", "perturbation": "Potentially disease-relevant; identity contract incomplete", "context": "DMD myoblast / source-study context under audit", "access_state": "AUTHOR_CONTACT_OR_ARCHIVE_RECOVERY_REQUIRED", "feature_metadata_state": "MISSING", "direct_dmd_candidate_outcome": false, "priority": "P0", "recommended_use": "Recover identifiers, columns, sample mapping and feature semantics before any reanalysis.", "next_action": "Request the exact feature table, sample metadata, perturbation identity mapping and processing description; checksum every returned file.", "source_url": "/resource/datasets/", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE288958-DMD-HUMAN-MUSCLE", "name": "GSE288958 human DMD/BMD/control muscle snRNA-seq and spatial context", "provider": "Jeon et al. / NCBI GEO", "data_class": "HUMAN_DMD_SINGLE_NUCLEUS_AND_SPATIAL", "scale": "11 human muscle samples: 5 control, 3 BMD and 3 DMD", "perturbation": "Disease and treatment-mechanism context; no candidate perturbation outcome", "context": "Human quadriceps/abdomen muscle biopsies with DMD, BMD and control groups", "access_state": "PUBLIC_GEO_AND_LOCAL_PROCESSED_ASSETS", "feature_metadata_state": "PUBLIC_MATRIX_AND_SAMPLE_METADATA", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Donor-resolved DMD cell-state signatures, context validation and treatment-mechanism stratification.", "next_action": "Preserve donor/sample units, harmonize cell-state labels and keep disease context separate from candidate perturbation response.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE277637-DMD-ORGANOID", "name": "GSE277637 DMD iPSC-derived skeletal-muscle organoid scRNA-seq", "provider": "Kindler et al. / NCBI GEO", "data_class": "HUMAN_DMD_ORGANOID_SINGLE_CELL", "scale": "4 10x samples: 1 healthy iPSC control and 3 DMD patient-derived iPSC lines", "perturbation": "DMD disease context; no candidate perturbation outcome", "context": "Human iPSC-derived skeletal-muscle organoids with myogenic progenitor/satellite-cell focus", "access_state": "PUBLIC_GEO_LOCAL_INGEST_AVAILABLE", "feature_metadata_state": "PUBLIC_RAW_MATRIX_WITH_SAMPLE_LABELS", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Organoid-specific DMD/control baseline and myogenic progenitor state validation.", "next_action": "Analyze as an organoid layer with line-aware units; do not pool it with patient biopsy muscle or call it a candidate screen.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE277637", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE293514-HUMAN-MYOBLAST-CROPSEQ", "name": "GSE293514 human-myoblast CROP-seq fusion screen", "provider": "Bi et al. / NCBI GEO", "data_class": "HUMAN_MYOBLAST_FUNCTIONAL_CROPSEQ", "scale": "57 samples; 250-hit mini-library; 3.7 GB count matrix and 36.3 MB deposited metadata", "perturbation": "Split-pool CROP-seq with GM, DM2d and DM6d myoblast differentiation states", "context": "Human myoblast fusion and early myogenic differentiation; not a DMD experiment", "access_state": "PUBLIC_GEO_TECHNICAL_RECONSTRUCTION_AVAILABLE", "feature_metadata_state": "AUTHOR_FEATURE_AND_GUIDE_IDENTITY_RECOVERY_REQUIRED", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Muscle-context safety/stress testing and prospective perturbation assay design, not DMD efficacy validation.", "next_action": "Resolve feature/guide identity before expression-level transfer; retain current gene-level fusion results only as a bounded safety filter.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE293514", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE273343-DMD-MOUSE-SATELLITE", "name": "GSE273343 DMD mouse satellite-cell scRNA-seq", "provider": "Granet et al. / NCBI GEO", "data_class": "MOUSE_DMD_SATELLITE_CELL_SINGLE_CELL", "scale": "4 sorted satellite-cell samples: B10, mdx, DBA and D2-mdx", "perturbation": "DMD genotype and regenerative-capacity context; no human candidate outcome", "context": "Mouse muscle satellite cells and myogenic progenitors", "access_state": "PUBLIC_GEO_RAW_MATRIX", "feature_metadata_state": "PUBLIC_SAMPLE_AND_CELL_MATRIX", "direct_dmd_candidate_outcome": false, "priority": "P2", "recommended_use": "Mechanistic satellite-cell module and cross-species state-direction stress test.", "next_action": "Use only as a species-specific layer with ortholog mapping and explicit mouse-to-human transfer limits.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE273343", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE265803-DMD-MOUSE-MACROPHAGE", "name": "GSE265803 DMD mouse resident-macrophage scRNA-seq", "provider": "Wang et al. / NCBI GEO", "data_class": "MOUSE_DMD_MACROPHAGE_SINGLE_CELL", "scale": "4 quadriceps/diaphragm samples across mdx5cv and Ccr2-related contexts", "perturbation": "DMD inflammatory-niche and resident-macrophage activation context", "context": "Mouse dystrophic skeletal-muscle immune niche", "access_state": "PUBLIC_GEO_RAW_MATRIX", "feature_metadata_state": "PUBLIC_SAMPLE_AND_CELL_MATRIX", "direct_dmd_candidate_outcome": false, "priority": "P2", "recommended_use": "Inflammatory-niche module and cell-state composition stress test.", "next_action": "Keep as a mouse immune-context layer; do not convert macrophage activation into candidate rescue evidence.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE265803", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-CELLXGENE-CENSUS-2025-11-08", "name": "CZ CELLxGENE Census LTS 2025-11-08", "provider": "Chan Zuckerberg Initiative", "data_class": "OBSERVATIONAL_SINGLE_CELL_CENSUS", "scale": "1,845 datasets; 162,025,130 human cells (99,633,637 unique)", "perturbation": "Predominantly observational; dataset dependent", "context": "Human, mouse and three primate species with standardized metadata", "access_state": "PUBLIC_API_AND_SOURCE_H5AD", "feature_metadata_state": "STANDARDIZED_WITH_SOURCE_LEVEL_VARIATION", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Find and register donor-resolved neuromuscular datasets; build disease-context slices and source-level citations.", "next_action": "Query muscle, myoblast, neuromuscular disease and donor metadata; reject datasets that cannot preserve donor-aware units.", "source_url": "https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_data_release_info.html", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-ARC-VIRTUAL-CELL-ATLAS", "name": "Arc Virtual Cell Atlas", "provider": "Arc Institute", "data_class": "OBSERVATIONAL_AND_PERTURBATIONAL_ATLAS", "scale": "More than 300 million cells across scBaseCount, Tahoe-100M and VCC resources", "perturbation": "Mixed observational, genetic and chemical resources", "context": "Broad public cell contexts", "access_state": "PUBLIC_OPEN_RESOURCES_WITH_DATASET_SPECIFIC_LICENSES", "feature_metadata_state": "RESOURCE_SPECIFIC_REVIEW_REQUIRED", "direct_dmd_candidate_outcome": false, "priority": "P2", "recommended_use": "Pretraining, representation and benchmark discovery—not DMD efficacy evidence.", "next_action": "Register only the exact constituent dataset used by a run, including version and license.", "source_url": "https://arcinstitute.org/news/arc-virtual-cell-atlas-launch", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-TAHOE-100M", "name": "Tahoe-100M", "provider": "Tahoe Bio / Vevo Therapeutics / Arc Institute", "data_class": "CHEMICAL_PERTURBATION_ATLAS", "scale": "Over 100 million profiles; 50 cancer cell lines; 1,100 small-molecule perturbations", "perturbation": "Small molecules with vehicle controls and drug metadata", "context": "Cancer cell lines", "access_state": "PUBLIC_HUGGING_FACE_CC0", "feature_metadata_state": "TABLES_AVAILABLE_REQUIRES_PLATE_AWARE_PROCESSING", "direct_dmd_candidate_outcome": false, "priority": "P2", "recommended_use": "Chemical-response scalability and context-generalization benchmark.", "next_action": "Start with streaming metadata and a small frozen subset; keep cancer-cell findings outside DMD claims.", "source_url": "https://huggingface.co/datasets/tahoebio/Tahoe-100M", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-ARC-VCC-H1-2025", "name": "Arc Virtual Cell Challenge H1 hESC benchmark", "provider": "Arc Institute", "data_class": "HELD_OUT_GENETIC_PERTURBATION_BENCHMARK", "scale": "Approximately 300,000 cells across 300 CRISPRi perturbations", "perturbation": "CRISPRi; 150 train, 50 validation and 100 held-out test perturbations", "context": "H1 human embryonic stem cells", "access_state": "PUBLIC_CHALLENGE_DATA_AND_RULES", "feature_metadata_state": "BENCHMARK_CONTRACT_AVAILABLE", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "First adapter target for STATE or another external model because the split and metrics are externally defined.", "next_action": "Reproduce simple baselines and metric formulas before running a complex adapter; preserve held-out boundaries.", "source_url": "https://arcinstitute.org/news/behind-the-data-virtual-cell-challenge", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-REPLOGLE-2022", "name": "Genome-scale Perturb-seq", "provider": "Replogle et al.", "data_class": "GENOME_SCALE_CRISPRI_PERTURB_SEQ", "scale": "Screens covering 9,866 expressed genes and 2,057 common-essential genes", "perturbation": "CRISPRi with direct guide capture", "context": "K562 and RPE1 cell systems", "access_state": "PUBLIC_PROCESSED_AND_ARCHIVAL_SOURCES", "feature_metadata_state": "PUBLIC_BUT_ADAPTER_HARMONIZATION_REQUIRED", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Genetic perturbation pretraining and frozen cross-context benchmarks.", "next_action": "Use a versioned processed object with explicit gene universe, control definition and cell-line split.", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9380471/", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-SCPERTURB-2024", "name": "scPerturb", "provider": "Sander Lab and collaborators", "data_class": "HARMONIZED_PERTURBATION_COLLECTION", "scale": "44 public single-cell perturbation-response datasets in the Nature Methods release", "perturbation": "Genetic, chemical and other targeted perturbations", "context": "Multiple assays and cell systems", "access_state": "PUBLIC_ZENODO_AND_SOURCE_CODE", "feature_metadata_state": "HARMONIZED_WITH_DATASET_LEVEL_LIMITATIONS", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Dataset discovery, preprocessing comparison and multi-dataset stress tests.", "next_action": "Screen every dataset for cell context, controls, replicate identity, licensing and leakage groups before use.", "source_url": "https://www.sanderlab.org/scPerturb/", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-DEPMAP-26Q1", "name": "DepMap Public 26Q1", "provider": "Broad Institute DepMap", "data_class": "CRISPR_DEPENDENCY_AND_MOLECULAR_CONTEXT", "scale": "Genome-wide CRISPR dependency plus expression, mutation and copy-number releases", "perturbation": "CRISPR knockout dependency", "context": "Cancer cell models", "access_state": "PUBLIC_PORTAL_DOWNLOADS_AND_EXPERIMENTAL_API", "feature_metadata_state": "VERSIONED_MODEL_AND_MAPPING_FILES_AVAILABLE", "direct_dmd_candidate_outcome": false, "priority": "P2", "recommended_use": "Contextual safety/dependency evidence and embedding input only.", "next_action": "Register exact release and model identifiers; never relabel cancer dependency as DMD muscle response.", "source_url": "https://depmap.org/portal/data_page/?tab=allData", "direct_dmd_candidate_truth": false } ], "priority_rule": "P0 closes an existing source-identity blocker. P1 enables a frozen benchmark or donor-resolved disease-context import. P2 expands scale or context but cannot replace direct disease outcomes.", "current_decision": "Recover author-missing feature/metadata first. In parallel, standardize GSE288958 and GSE277637 as donor/line-aware disease-context objects, keep GSE293514 as a bounded muscle screen, prepare a VCC/Replogle-compatible benchmark adapter, and query CELLxGENE for additional donor-resolved neuromuscular datasets.", "direct_dmd_candidate_perturbation_dataset_count": 0, "claim_boundary": "Large public corpora may support pretraining, context or benchmarking. None of the listed external opportunities is qualifying candidate-level DMD perturbation outcomes." }