CGIG_HEAT24H_RNASEQ_PRJNA407831

Primary-analysis sample count: 23. The counted unit and independent experimental units are described under Biological replication; counts may represent animals, pools or libraries.

Treatment

Held in 35 C seawater (sublethal) for 24 h

Control

Same tanks sampled at 0 h, before the temperature was raised (laboratory acclimation 14.2-18.2 C)

Biological replication

23 libraries analysed (24 sequenced; one 0 h outlier left out): 11 at 0 h and 12 at 24 h. Each library pools equal gill RNA from five oysters of one culture tank; four populations (two sites x intertidal or subtidal origin) x three tanks, and the same tanks are sampled at each time.

Phenotype interpretation

Intertidal-origin F1 oysters showed higher survival after acute heat stress (42 C, 1 h) and higher metabolic rates at 35 C than subtidal-origin oysters, with slower growth, and more transcriptional plasticity. AREE records the gill transcriptional response to 35 C averaged over the four populations, not survival per library.

Analysis status

raw_reanalysis_harmonized

Quality control and results

All 36 pooled gill libraries (573,193,161 read pairs) quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping rates 65.5-73.8% (median 72.0%; 0 h 70.7%, 6 h 72.4%, 24 h 72.4%). Expressed-SNP allele frequencies at 1,464 sites show no resequenced RNA: pools within a population and time differ by 0.108 or more (mean 0.170) against 0.044 for one RNA resequenced, and pools are closer within a population (0.171) than between populations (0.202), the genetic structure that the population block absorbs. h0_LTJ_2 is an outlier (median VST correlation 0.906-0.908 against a cut-off of 0.957) and is left out; it is the library the publication discarded (LT-I_0h_2), which ties LTJ to the Laoting intertidal population. ~ population + condition (11 v 12): 2,714 of 23,282 tested genes reach FDR < 0.05 (1,363 higher, 1,351 lower at 24 h); the tank-paired model gives 2,058, all significant genes keep their direction and log2 fold changes correlate 0.913. Heat shock protein 68 genes (log2FC up to 7.6), BAG3 and alpha-crystallin remain high, and the response broadens from 6 h, consistent with the publication’s delayed large-scale plasticity; 434 genes are significant at both 6 and 24 h.

Limitations

  • Both AREE records from this study (the other is CGIG_HEAT6H_RNASEQ_PRJNA407831, 6 h) test against the same twelve 0 h pools, so they carry the dependence group PRJNA407831_0h_pools and count as one replication group.
  • Each library pools gill RNA of five oysters, so the error model describes tank-pool variation, not variation between animals. The sister IOCAS study PRJNA826964 deposited resequenced RNA as replicates, so these pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
  • The model blocks on the four source populations (~ population + condition), so the effect is averaged over intertidal and subtidal origins and the two sites; the publication’s main result, that intertidal oysters respond with more plasticity, is not part of this record. A tank-paired model (~ tank + condition) is kept as a sensitivity analysis.
  • Sample aliases code tidal origin as J or X (for example BYQJ01, LTX243); the publication uses I (intertidal) and S (subtidal), and the BioSamples do not record it. J and X are read as the Chinese jian (intertidal) and xia (subtidal), but no AREE result depends on that reading because population is a blocking factor.
  • One 0 h library, h0_LTJ_2, is left out by AREE’s QC rule (median VST correlation below the median minus three robust SDs); it is the library the publication also discarded (LT-I_0h_2). The exclusion lives in scripts/prepare_prjna407831_fastqs.py.
  • ENA served other studies at 0.05-0.35 MB/s in October 2026, so all runs come from NCBI .sra archives checked against NCBI’s MD5s, with read counts checked against the manifest on conversion.

Sources