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"asset_id": "RESULT:gse297388_annotation_source_triage_v01", "layer": "analysis", "title": "GSE297388 Annotation Source Triage V01", "identifier": "gse297388_annotation_source_triage_v01", "disease": "DMD", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_annotation_source_triage_v02", "layer": "analysis", "title": "GSE297388 Annotation Source Triage V02", "identifier": "gse297388_annotation_source_triage_v02", "disease": "DMD", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_author_label_contract_v01", "layer": "analysis", "title": "GSE297388 Author Label Contract V01", "identifier": "gse297388_author_label_contract_v01", "disease": "DMD", 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"/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_spatial_context_embedding_baseline_v01", "layer": "analysis", "title": "GSE297388 Spatial Context Embedding Baseline V01", "identifier": "gse297388_spatial_context_embedding_baseline_v01", "disease": "DMD", "modality": "spatial / representation", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/cell-browser/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_spatial_context_knn_stability_v01", "layer": "analysis", "title": "GSE297388 Spatial Context Knn Stability V01", "identifier": "gse297388_spatial_context_knn_stability_v01", "disease": "DMD", "modality": "spatial / representation", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/cell-browser/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_spatial_context_negative_controls_v01", "layer": "analysis", "title": "GSE297388 Spatial Context Negative Controls V01", "identifier": "gse297388_spatial_context_negative_controls_v01", "disease": "DMD", "modality": "spatial / representation", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/cell-browser/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_spatial_gbtissue_composition_gate_v01", "layer": "analysis", "title": "GSE297388 Spatial Gbtissue Composition Gate V01", "identifier": "gse297388_spatial_gbtissue_composition_gate_v01", "disease": "DMD", "modality": "spatial / representation", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/cell-browser/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:gse297388_spatial_preflight_v01", "layer": "analysis", "title": "GSE297388 Spatial Preflight V01", "identifier": "gse297388_spatial_preflight_v01", "disease": "DMD", "modality": "spatial / representation", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/cell-browser/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:high_quality_upgrade", "layer": "analysis", "title": "High Quality Upgrade", "identifier": "high_quality_upgrade", "disease": "Cross-context", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:model_intelligence_execution_v01", "layer": "analysis", "title": "Model Intelligence Execution V01", "identifier": "model_intelligence_execution_v01", "disease": "Cross-context", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:multidisease_release_v01", "layer": "analysis", "title": "Multidisease Release V01", "identifier": "multidisease_release_v01", "disease": "Multi-disease", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:multidisease_release_v02", "layer": "analysis", "title": "Multidisease Release V02", "identifier": "multidisease_release_v02", "disease": "Multi-disease", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:nar_measured_dmd_evidence_v01", "layer": "analysis", "title": "Nar Measured Dmd Evidence V01", "identifier": "nar_measured_dmd_evidence_v01", "disease": "DMD", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "RESULT:site_deployment_v109", "layer": "analysis", "title": "Site Deployment V109", "identifier": "site_deployment_v109", "disease": "Cross-context", "modality": "derived analysis", "state": "ANALYSIS_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Traceable local analysis family retained in the project workspace." }, { "asset_id": "MODEL:cellspatialfoundation", "layer": "model", "title": "Cellspatialfoundation", "identifier": "cellspatialfoundation", "disease": "Cross-context", "modality": "model code / checkpoint", "state": "MODEL_ASSET_AVAILABLE", "public_route": "/resource/models/", "purpose": "Local model or checkpoint asset; execution and disease applicability are audited separately." }, { "asset_id": "MODEL:nicheformer", "layer": "model", "title": "Nicheformer", "identifier": "nicheformer", "disease": "Cross-context", "modality": "model code / checkpoint", "state": "MODEL_ASSET_AVAILABLE", "public_route": "/resource/models/", "purpose": "Local model or checkpoint asset; execution and disease applicability are audited separately." }, { "asset_id": "PUBLICATION:CURATED-V08-5", "layer": "publication", "title": "Curated v08.5 semantic-contract working package", "identifier": "curated_v08_5", "disease": "Multi-disease", "modality": "manuscript · figures · tables · evidence-governance schema", "state": "CURATED_WORKING_NOT_SUBMISSION_READY", "public_route": "/resource/diseases/", "purpose": "Current working manuscript, figures, supplement, schema and website consistency contract; not submission-ready." }, { "asset_id": "API:PUBLIC-RESOURCE", "layer": "api", "title": "Public website and typed API", "identifier": "public/resource", "disease": "Multi-disease", "modality": "HTML · JSON · TSV · schemas", "state": "PUBLISHED", "public_route": "/resource/api", "purpose": "Publicly navigable research objects, manifests, schemas and downloads." }, { "asset_id": "GAP:DMD-PERTURBATION-OUTCOME", "layer": "missing", "title": "Matched candidate-level DMD perturbation outcomes", "identifier": "DMD-PERTURBATION-OUTCOME", "disease": "DMD", "modality": "planned molecular + functional outcomes", "state": "DECISION_CRITICAL_GAP", "public_route": "/resource/planner", "purpose": "Required to pilot-test disease-conditioned virtual-cell counterfactual assignment." }, { "asset_id": "SERVER:DMD-SINGLE-CELL", "layer": "server", "title": "Integrated DMD single-cell analysis", "identifier": "DMD-SINGLE-CELL", "disease": "DMD", "modality": "single-cell · pseudobulk", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "annotated objects and cell-type differential results" }, { "asset_id": "SERVER:DMD-SEMA3C", "layer": "server", "title": "DMD SEMA3C single-cell and spatial program", "identifier": "DMD-SEMA3C", "disease": "DMD", "modality": "single-cell · spatial · NicheNet", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "state-resolved and cell-communication analyses" }, { "asset_id": "SERVER:CROSS-SPECIES", "layer": "server", "title": "Human, mouse and macaque model-validity assets", "identifier": "CROSS-SPECIES", "disease": "DMD", "modality": "cross-species h5ad", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "SATURN and TranscriptFormer-ready counts" }, { "asset_id": "SERVER:VIRTUAL-CELL", "layer": "server", "title": "Virtual-cell execution workspace", "identifier": "VIRTUAL-CELL", "disease": "Cross-context", "modality": "STATE · baselines · candidate screens", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "66 result families and 2,278 result files" }, { "asset_id": "SERVER:CLINICAL-DMD", "layer": "server", "title": "Controlled clinical DMD matrix collection", "identifier": "CLINICAL-DMD", "disease": "DMD", "modality": "patient 10x matrices", "state": "CONTROLLED_METADATA_ONLY", "public_route": "/resource/data-universe/", "purpose": "Collection-level availability only; individual files, paths and subject metadata are withheld." }, { "asset_id": "SERVER:RAW-VALIDATION", "layer": "server", "title": "Large external validation archives", "identifier": "RAW-VALIDATION", "disease": "DMD", "modality": "FASTQ · STARsolo · SRA", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "retained for reproducibility; not required for current site rendering" }, { "asset_id": "SERVER-PRIORITY:001", "layer": "server", "title": "Celltype Final Pseudobulk Delta De All", "identifier": "SRV-DATA-001", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Cell-type-level DMD pseudobulk delta/DE table; best first sync." }, { "asset_id": "SERVER-PRIORITY:002", "layer": "server", "title": "Baseline Pseudobulk S Vs C DE All Celltypes", "identifier": "SRV-DATA-002", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Group-aware baseline pseudobulk DMD-vs-control DE." }, { "asset_id": "SERVER-PRIORITY:003", "layer": "server", "title": "Source State Pseudobulk Counts", "identifier": "SRV-DATA-003", "disease": "DMD", "modality": "tsv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Source-state pseudobulk counts for state-level DMD signal." }, { "asset_id": "SERVER-PRIORITY:004", "layer": "server", "title": "Target State Dmd Vs Wt De Summary", "identifier": "SRV-DATA-004", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Compact DMD-vs-WT target-state DE summary." }, { "asset_id": "SERVER-PRIORITY:005", "layer": "server", "title": "Target State All Gene Pseudobulk", "identifier": "SRV-DATA-005", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "All-gene target-state pseudobulk matrix." }, { "asset_id": "SERVER-PRIORITY:006", "layer": "server", "title": "Limma Delta DiD All Celltypes", "identifier": "SRV-DATA-006", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Alternative limma delta-DiD table." }, { "asset_id": "SERVER-PRIORITY:007", "layer": "server", "title": "*", "identifier": "SRV-DATA-007", "disease": "DMD", "modality": "rds", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "Cell-type-specific pseudobulk count RDS files." }, { "asset_id": "SERVER-PRIORITY:008", "layer": "server", "title": "DESeq2 * DMD Vs WT", "identifier": "SRV-DATA-008", "disease": "DMD", "modality": "csv", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "State-specific DMD-vs-WT DESeq2 outputs." }, { "asset_id": "SERVER-PRIORITY:009", "layer": "server", "title": "Seurat Qc Harmony Annotated Final V1", "identifier": "SRV-DATA-009", "disease": "DMD", "modality": "rds", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Main annotated integrated DMD Seurat object; useful but larger and R-dependent." }, { "asset_id": "SERVER-PRIORITY:010", "layer": "server", "title": "Seurat Raw Merged", "identifier": "SRV-DATA-010", "disease": "DMD", "modality": "rds", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Raw merged Seurat object." }, { "asset_id": "SERVER-PRIORITY:011", "layer": "server", "title": "GSE156497 Merged Raw Rebuilt 20260604", "identifier": "SRV-DATA-011", "disease": "DMD", "modality": "h5ad", "state": "READY_FOR_ANALYSIS", "public_route": "/resource/data-universe/", "purpose": "External validation AnnData object." }, { "asset_id": "SERVER-PRIORITY:012", "layer": "server", "title": "Prjna772047 Human Muscle Phase41 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"public_route": "/resource/data-universe/", "purpose": "Macaque SATURN/TranscriptFormer-ready counts." }, { "asset_id": "SERVER-PRIORITY:016", "layer": "server", "title": "*", "identifier": "SRV-DATA-016", "disease": "DMD", "modality": "h5ad", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Human dystrophinopathy Visium/CellxGene spatial assets." }, { "asset_id": "SERVER-PRIORITY:017", "layer": "server", "title": "GSE135893 Matrix.Mtx", "identifier": "SRV-DATA-017", "disease": "DMD", "modality": "mtx.gz", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Large public DMD matrix; requires metadata harmonization." }, { "asset_id": "SERVER-PRIORITY:018", "layer": "server", "title": "GSE288958 RAW", "identifier": "SRV-DATA-018", "disease": "DMD", "modality": "tar", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "GSE288958 raw package." }, { "asset_id": "SERVER-PRIORITY:019", "layer": "server", "title": "Human Gse288958 Counts Genes By Cells", "identifier": "SRV-DATA-019", "disease": "DMD", "modality": "mtx", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "GSE288958 exported counts matrix." }, { "asset_id": "SERVER-PRIORITY:024", "layer": "server", "title": "DS03 PRJNA772047", "identifier": "SRV-DATA-024", "disease": "DMD", "modality": "fastq+starsolo", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Human Duchenne vs healthy; avoid first full sync." }, { "asset_id": "SERVER-PRIORITY:025", "layer": "server", "title": "DS02 PRJNA1218493", "identifier": "SRV-DATA-025", "disease": "DMD", "modality": "fastq+starsolo", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Human DMD/normal; avoid first full sync." }, { "asset_id": "SERVER-PRIORITY:026", "layer": "server", "title": "Prjna771932 Lite Rescue 20260612", "identifier": "SRV-DATA-026", "disease": "DMD", "modality": "sra", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Mouse mdx/WT SRA; use only if reprocessing is needed." }, { "asset_id": "SERVER-PRIORITY:027", "layer": "server", "title": "Matrix", "identifier": "SRV-DATA-027", "disease": "DMD", "modality": "mtx", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Mouse mdx STARsolo raw matrix." }, { "asset_id": "SERVER-PRIORITY:028", "layer": "server", "title": "Matrix", "identifier": "SRV-DATA-028", "disease": "DMD", "modality": "mtx", "state": "SERVER_AVAILABLE", "public_route": "/resource/data-universe/", "purpose": "Mouse mdx STARsolo raw matrix." } ], "claim_boundary": "This projection exposes catalog metadata, not controlled matrices or permission to access them." }