[study] ZWU2022_VIBRIO_TIMECOURSE (PRJNA852380)

[sr320]

Claimed 2026-10-14; run, QC and harmonization finished 2026-10-16. Ready for review: no dependency on other open PRs; the scope check passes, and the branch is synced with main.

Study

• study_id: ZWU2022_VIBRIO_TIMECOURSE
• Accession: PRJNA852380 (Zhejiang Wanli University). No publication found.
• Design (from the deposit): 9-month-old intertidal oysters (Qingdao), digestive gland. Untreated controls and 1, 3, 6, 12 and 24 h after Vibrio exposure, n = 3 each, 18 distinct BioSamples.
• Replicates screened before download: an expressed-SNP check on ~250 MB of reads from five libraries found within-group 0.196 against 0.054 one-RNA noise, so these are different animals.

Result (each time point vs untreated controls)

Comparison	padj < 0.05
1 h	91 / 27,179
3 h	132 / 27,034
6 h	250 / 26,998
12 h	1,230 / 27,049
24 h (meta_analysis_primary)	3,351 / 27,063

• A building response: it grows steadily over time, mostly up-regulated, and adjacent time points agree (fold-change r = 0.55–0.61).
• Replicates pass: dispersion 0.0067–0.011.
• Run: mapping 78.4–80.8% (IU), on main's code.
• Harmonized: 135,323 evidence records.

Caveats (passed_with_warnings)

• No paper: the Vibrio species, dose and route are unknown and left null.
• No outcome deposited: flagged ambiguous_phenotype_definition.
• Controls are one untreated group, not time-matched.

Run notes

• One stubborn file: SRR19849552_1 failed five aria2 attempts, but a plain single-stream curl copy matched ENA's MD5.
• Disk full: the first attempt stopped when the data drive filled; it was freed and the run resumed.

Checklist

• aree validate-study passes
• Sample sheet from aree fetch-samplesheet (aliases → group); matches BioSample isolate
• All 36 FASTQ MD5s verified against ENA
• Manifests, standardized tables, reports, dispersion and genotype checks committed
• qc_status: passed_with_warnings, analysis_status: harmonized
• Curation tests in tests/test_zwu2022_vibrio_timecourse.py (5)
• No edits to shared code

🤖 Generated with Claude Code