CGIG_HEAT12H_RNASEQ_PRJNA1244231

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

Seawater-injected oysters at 12 h, read from the sample-name code SW-12 as 12 h of heat stress

Control

Seawater-injected oysters at 0 h (sample-name code SW-0)

Biological replication

6 gill libraries: 3 at 0 h and 3 at 12 h. By expressed-SNP genotype each group’s three libraries are one RNA pool sequenced three times, so the effective design is one pool against one pool.

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 12 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 70.7-73.2%. The sample-name reading is supported by heat-shock induction: summed heat shock protein 70 TPM rises 3.4-fold from 0 h to 12 h in seawater-injected oysters (2.1-fold with the ERK inhibitor), with individual HSP70 genes up to log2FC 9.2. Expressed-SNP allele frequencies at 3,136 sites show that the three libraries within each group are indistinguishable from one RNA resequenced (mean difference 0.053 within groups against 0.051 expected, correlation 0.92) while groups are genetically distinct pools (0.178 between groups); summed HSP70 TPM also differs by under 1% between libraries within a group. ~ condition (3 v 3) gives 12,303 of 23,144 tested genes at FDR < 0.05 (53%), a count driven by technical replication and the genetic difference between pools, so the record is not harmonized.

Limitations

  • No publication describes this BioProject. The related study from the same laboratory (Wang et al. 2024, Cell Commun Signal, doi:10.1186/s12964-024-01923-0) used BioProjects PRJNA1059049 and PRJNA1058704; it pools gill RNA from 5 oysters per replicate and uses 42 C as the sublethal heat dose. The BioSamples record no temperature or duration; ‘0’ and ‘12’ are read as hours of heat stress from the sample names (SW-0-n, SW-12-n) and checked against heat-shock gene induction in the data.
  • The BioProject also contains an ERK-inhibitor arm (ERK-0, ERK-12); it is pharmacological and is not an AREE record.
  • 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 2026-10-10): each group’s three libraries are one RNA pool sequenced three times, so DESeq2 dispersion reflects sequencing noise only, and heat cannot be separated from the genetic difference between the 0 h and 12 h pools. Collapsing to one library per group leaves 1 v 1, which cannot be tested. The DESeq2 results are kept outside the repository.

Sources