[study] LI2018_HEAT_TIDAL (PRJNA407831)

[sr320]

Claimed by aree start-study on Hete, 2026-10-11. Run, QC and harmonization finished 2026-10-13. Ready for review: no dependency on other open PRs, and the scope check passes.

Study

• study_id: LI2018_HEAT_TIDAL
• Accession: PRJNA407831. The paper is Li et al. 2018, Front Physiol 9:825, 10.3389/fphys.2018.00825, open access; methods read in full.
• Design: common-garden F1 of four wild populations (two Bohai Sea sites × intertidal / subtidal origin), three tanks each, 35 °C for 24 h. Gill of 5 oysters per tank is pooled into one library at 0, 6 and 24 h (36 libraries). The authors' outlier LT-I_0h_2 (alias LTJ02) is excluded throughout.
• Measured, heritable tolerance: intertidal-origin F1 survived a 42 °C heat shock better than subtidal at both sites (Kaplan–Meier, p < 0.05).

Result

Comparison	Arms	padj < 0.05
35 °C 24 h vs 0 h (meta_analysis_primary)	12 v 11 tanks	2,483 / 29,628
35 °C 6 h vs 0 h	12 v 11 tanks	768 / 29,849
intertidal vs subtidal, 0 h (resilience)	2 v 2 populations (--replicate_unit population)	99 / 28,221

• Harmonized: 87,698 evidence records.
• Run: mapping 69.2–78.1% (ISR); first comparison 114/114 tasks, the others reuse its quantifications.

QC: low dispersion, settled by genotypes

The dispersion screen read low (7 of 12 groups under its 0.005 floor). That floor is calibrated on single animals, and each library here pools 5 sibling oysters.

An expressed-SNP check on the 23 libraries at 0 h and 24 h (1,925 sites, replicate_genotype_check.txt) settles it. Pools within a group differ by 0.177 on average and never less than 0.112, against 0.047 for one RNA sample sequenced twice. Every pool is different animals, and pools within a population are a bit more alike than between, as siblings should be.

Curation decisions

• The 24 h heat contrast is the primary (prespecified). It can pool with GEORGE2023 ([study] GEORGE2023_HEATWAVE_PLOIDY (PRJNA913164) #18) and LIU2019 ([study] LIU2019_HEAT_HSF1 (PRJNA516762) #37).
• The tidal-origin contrast is the first real resilience comparison in this batch. Replication is honest: 2 v 2 populations, flagged family_level_replication.
• Tidal-zone code J = intertidal: read from pinyin, and corroborated because the authors' excluded library LT-I_0h_2 is alias LTJ02.
• Control caveat: the heat contrasts' control is the same tanks before heating, not a concurrent unheated group.

Checklist

• aree validate-study passes (expected stress_response override warnings)
• Sample sheet from aree fetch-samplesheet; hours and site cross-checked against the BioSample temp / isolate attributes
• All 72 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_li2018_heat_tidal.py (9)
• No edits to shared code

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