CGIG_HEAT42_RNASEQ_PRJNA1511593
Primary-analysis sample count: 6. The counted unit and independent experimental units are described under Biological replication; counts may represent animals, pools or libraries.
Treatment
Heat, read from the sample-name code H42H1 as 42 C for 1 h
Control
Control gill (sample-name code H0)
Biological replication
6 gill libraries: 3 controls and 3 42 C for 1 h. Each library is a pool by expressed-SNP genotype; pool size is not recorded.
Phenotype interpretation
No phenotype is deposited and no publication is linked; AREE records the gill transcriptional response to acute heat.
Analysis status
raw_reanalysis_complete_not_harmonized
Quality control and results
All 9 GG gill libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 68.7-69.5% by group. The sample-name reading is confirmed by heat-shock induction: heat shock protein 68 genes rise up to log2FC 10.6 at 37 C for 12 h and 8.5 at 42 C for 1 h, with BAG3 and the Hsp90 co-chaperone Cdc37. Expressed-SNP allele frequencies at 2,523 sites show every library is a pool and that the three groups are genetically distinct (mean difference 0.187 between groups against 0.072 within, 0.049-0.052 expected for one RNA resequenced), so heat is confounded with genetic background; the modest excess within groups also leaves open that a group’s three pools are subsamples of one batch. ~ condition (3 v 3) gives 14,382 of 21,576 tested genes at FDR < 0.05 (67%), a count inflated by the genetic difference between groups, so the record is not harmonized.
Limitations
- No publication is linked, and PubMed searches on 2026-10-09 found none. The BioSamples record no temperature or duration, and the BioProject describes the samples as ‘under normal conditions’. The treatments are read from the sample names (GGH0S = control, GGH37H12S = 37 C for 12 h, GGH42H1S = 42 C for 1 h) and checked against heat-shock gene induction in the data, recorded in the quality-control summary.
- The two AREE records from this study (37 C for 12 h and 42 C for 1 h) test against the same three control libraries; neither is harmonized.
- The BioProject also contains a backcross line (BC3, deposited as Crassostrea sp.); AREE uses only the Magallana gigas (GG) libraries.
- All runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the NCBI spot counts on conversion.
- Not harmonized into the evidence base (decision 2026-10-09): the control, 37 C and 42 C groups are genetically distinct sets of oysters (allele-frequency difference 0.187 between groups against 0.072 within), so heat cannot be separated from genetic background, and the resulting gene counts (37% and 67% of tested genes) are not credible as a heat response. The heat-shock induction confirms the treatments. The DESeq2 results are kept outside the repository.