# GSE288958 reference QC and independent-audit closure

- Status: **REFERENCE_CONTEXT_AUDIT_COMPLETE_AMBIENT_AND_AUTHOR_EXACT_REPROCESSING_OPEN**
- Checked: 2026-09-09
- Context release blocking open gates: **0**
- Enhancement gates still open: **ambient_rna, author_exact_reprocessing**

## Source and denominators

GEO 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.

## Independent doublet audit

Donor-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.

## Independent annotation audit

Fixed 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.

## Remaining boundaries

- Ambient RNA remains open because the released matrices do not identify empty droplets.
- The exact author command, read structure, whitelist, reference checksum, sample sheet and FASTQ aggregation manifest remain unavailable.
- Subject identity is represented by one GSM/BioSample biopsy unit; cells remain nested observations.
- Disease-effect testing and direct candidate-level DMD perturbation truth remain locked.

## 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.