[study] LIU2019_HEAT_HSF1 (PRJNA516762)

[sr320]

Claimed by aree start-study on Hete, 2026-10-12. Run, QC and harmonization finished 2026-10-12. Ready for review: no dependency on other open PRs, and the scope check passes locally.

Study

• study_id: LIU2019_HEAT_HSF1
• Accession: BioProject PRJNA516762. The paper is Liu et al. 2019, BMC Genomics 20:639, 10.1186/s12864-019-6003-8, open access.
• Design: 7-month-old oysters, gill, heat shock at 35 °C for 2 h vs untreated control. 3 pooled libraries (5 oysters each) per group. The paper's HSF1-RNAi groups are deposited too but not used.
• Why this one: its 6 control and heat-shock runs were already staged on this machine from an earlier AREE-co pass, so it ran on idle CPU while the other queued studies waited on slow ENA downloads. All 12 FASTQ files matched ENA's MD5s first.
• Mode: raw_reanalysis, paired-end, native run (Nextflow 26.04.7, 24/24 tasks).

Result

Genes at padj < 0.05	111 / 28,333 (58 up)
Median lfcSE (baseMean > 100)	0.19
Mapping	77.7–79.8% (IU)
Harmonized evidence records	28,333

Heat shock protein 68 is among the most significant induced genes (log2FC 4.4).

QC: borderline dispersion, settled by genotypes

The dispersion screen flagged the control pools at 0.0049, just under its 0.005 floor (heat shock: 0.0077). That floor is calibrated on single-animal libraries, and pooling 5 oysters lowers dispersion about fivefold by itself.

An expressed-SNP check (3,244 sites, replicate_genotype_check.txt) settles it. Pools within a group differ in allele frequency by 0.188, against 0.054 for one RNA sample sequenced twice, and as much as pools from different groups do. So they are different animals. By contrast, IOCAS2024 (#17) failed at 0.061 vs 0.051.

Curation decisions

• Classification: stress_response on thermal_tolerance; no tolerance outcome was measured.
• Warnings recorded: sequenced animals were selected by HSF1 qPCR ("according to the analysis of HSF1 expression"), and container structure isn't described, so a group may have shared one container.
• Pooling: meta_analysis_primary is set on the only comparison. It joins the thermal pool with GEORGE2023 ([study] GEORGE2023_HEATWAVE_PLOIDY (PRJNA913164) #18) and LI2018 ([study] LI2018_HEAT_TIDAL (PRJNA407831) #28). They differ in life stage and exposure, which the meta-analysis should stratify.

Checklist

• aree validate-study passes (expected stress_response override warning)
• Sample sheet from aree fetch-samplesheet (design parsed from the sample aliases)
• FASTQ MD5s verified against ENA
• Workflow manifest, standardized table and HTML report committed; no raw reads, work/ or results/
• qc_status: passed_with_warnings, analysis_status: harmonized
• Curation tests: 4 (full suite 348)
• No edits to shared code

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