[study] PAYTON2017_HAB_AMINUTUM (PRJEB18614)

[sr320]

Claimed by aree start-study on Hete, 2026-10-11. Merged as a registration (2026-10-17); the RNA-seq run is still pending.

Study

• study_id: PAYTON2017_HAB_AMINUTUM, AREE's first harmful_algal_bloom study
• Accession(s): ENA PRJEB18614 = ArrayExpress E-MTAB-5345; DOI 10.1038/s41598-017-03797-4
• Mode: raw_reanalysis, not yet run
• Machine and storage used: none yet

What this merges

• Registration: adult gill after 6 days on toxic Alexandrium minutum vs non-toxic Heterocapsa triquetra. 52 runs = 26 pooled libraries (13 per diet) × 2 lanes, sampled every 4 h over 52 h. Every library pools animals from all three tanks of its diet, so it's flagged tank_level_replication. Toxin exposure was confirmed, but no tolerance outcome was measured, so the comparison is stress_response on toxicant_tolerance.
• Run inputs: sample sheet and FASTQ manifest from aree fetch-samplesheet, the ArrayExpress SDRF (the only source of sampling times), and the run config.
• Status set to not_started: both status fields previously said in_progress. No run is under way and results_file is null; a test pins this.

Checklist

• aree validate-study passes (one documented override: stress_response)
• Sample sheet and FASTQ manifest generated by aree fetch-samplesheet
• FASTQ MD5s verified, workflow manifests, results and report: pending the run (follow-up study PR)
• qc_status / analysis_status reflect what was actually done: not_started
• Limitations and flags recorded (tank-level replication, time of day not modelled, control alga differs beyond toxicity)
• Curation tests: tests/test_payton2017_hab_aminutum.py. Full suite on current main: 737 passed.
• Only this study's files (check-study-scope passes); the toxicant_tolerance term came from Add a toxicant_tolerance phenotype term (ontology 0.3.0) #31

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