# GSE288958 formal QC gate

- Status: **REFERENCE_CONTEXT_READY_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN**
- Checked: 2026-08-12T18:15:46+0800
- Source object: `ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8`
- Context-release blocking open gates: **0**

## Current decision

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.

## Denominator reconciliation

- Raw matrix inventory: **61,189** cells
- Formal matrix-QC broad gate: **59,237** cells
- Pilot RDS: **59,222** cells
- Raw minus pilot: **1,967** cells

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.

## Gate table

| Gate | State | Evidence | Closure required |
|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |

## Independent audits

Donor-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.

## Allowed use

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.

Direct DMD candidate perturbation truth remains **0/21**.