[study] TUCCI2025_HEAT_PRIMING (PRJNA1132140)

[sr320]

Claimed by aree start-study on Pori, 2026-10-12. Run finished 2026-10-13.

Study

• study_id: TUCCI2025_HEAT_PRIMING, the first real clam study and the first real non-oyster study.
• Accession(s): PRJNA1132140. The publication is Tucci et al. 2025, iScience 28:113108 (10.1016/j.isci.2025.113108), whose data statement names this BioProject.
• Mode: raw_reanalysis.
• Machine and storage used: Pori. The reference bundle GCF_026571515.1 is fetched and verified on ~/aree-data/reference. No FASTQ is staged yet (13.8 GB).

Status: reanalyzed and harmonized (2026-10-13); ready for review

Both prespecified comparisons were run natively on Pori with tag_seq = true and fitted on clams. Tank, the unit of treatment, is not modelled (tank_level_replication).

Comparison	Genes	padj < 0.05	Classification
Naive: heatwave vs control (meta_analysis_primary)	28,984	1,606 (632 up, 974 down)	exposure_only
Heatwave: primed vs naive	28,291	24 (13 up, 11 down)	resilience

• Upper bounds. Both counts are upper bounds because tank is not modelled. The small primed-vs-naive count fits the survivor caveat: the naive heatwave arm is the 75% of naive clams that survived.
• Manifests. Both record tag_seq: true and length_model "none: counts without length offsets (tag_seq)", with 10 vs 10 clams and residual df 18. Every reference file matches the GCF_026571515.1 bundle provenance, and there are no warnings.
• Replicate dispersion QC passes in all four groups, with median dispersion 0.08 to 0.12 (the technical-replicate threshold is 0.005).
• Salmon mapped only 42 to 49% of reads. That is consistent with 3′ tags falling beyond annotated transcript ends on this contig-level assembly, and it is recorded under limitation (1).
• Harmonization: every gene resolves exact against rphil_gene_id_crosswalk.tsv, with a real standard error on every record.
• Download. ENA throttled this machine for most of a day. All 40 FASTQs were eventually verified against ENA's MD5s.

This is the first real non-oyster evidence in AREE. It forms the Manila clam partition (taxid 129788). Pooling within the species (k = 2) needs the second Padova heatwave study, PRJNA906528; check its library type and independence first.

Checklist

• aree validate-study registry/studies/TUCCI2025_HEAT_PRIMING.yaml passes. The one warning is the documented exposure_only override.
• Sample sheet and FASTQ manifest generated by aree fetch-samplesheet, not hand-written
• FASTQ MD5s verified against the manifest before the run
• Workflow manifest(s) committed under data/studies/TUCCI2025_HEAT_PRIMING/, with parameters, tool versions and input checksums
• Standardized result tables and the HTML report committed; no raw reads, work/ or results/
• qc_status and analysis_status in the YAML reflect what was actually run (qc_status: passed_with_warnings, analysis_status: harmonized)
• Limitations and quality flags record anything that weakens the evidence (replication, phenotype definition, excluded samples)
• Curation tests in tests/test_tucci2025_study.py pin the decisions that are easy to erode later
• No edits to shared code, vocabularies or docs; those went in a separate PR

Curation decisions

• 16S runs excluded. The BioProject holds 40 RNA-seq and 40 16S amplicon runs from the same RNA under the same attributes. Only library_strategy RNA-Seq is kept. Here the AMPLICON label is correct, unlike LUTIER2022's: the amplicon runs are paired-end, and the RNA-seq runs are 76 bp single-end at about 7 M reads, matching the paper.
• Two comparisons, prespecified before any run:
  • Naive heatwave vs naive control: exposure_only, meta_analysis_primary. This is the contrast that can pool with other Manila clam heat studies.
  • Primed vs naive under the same heatwave: resilience. According to the paper, about 4% of primed and 25% of naive clams died. That is a group-level survival difference, and no sequenced clam was scored for its own tolerance.
• Survivors only. RNA was taken on day 46, 15 days after the heatwave. The naive heatwave arm is therefore the surviving three-quarters of naive clams, which biases primed vs naive toward the null.
• Tank-level replication. There were two 25 L tanks per condition, but tank membership is not deposited, so DESeq2 cannot be fitted on tanks. The study carries tank_level_replication and records biological_replicates: 2. Ask the authors for tank IDs before running.
• Mapping: digestive gland maps to digestive_gland, and adults (26 mm, hatchery stock from SATMAR) map to adult. Identifiers are standardized against the RefSeq annotation GCF_026571515.1-RS_2023_10, not the authors' Xu et al. genome.
• Pooling partner. PRJNA906528 comes from the same Padova group. Confirm the animals are separate before counting it as a second study.

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