CGIG_HEAT6H_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 6 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 6 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): 935 of 23,666 tested genes reach FDR < 0.05 (537 higher, 398 lower at 6 h); the tank-paired model gives 664, all significant genes keep their direction and log2 fold changes correlate 0.925. Heat shock protein 68 genes rise up to log2FC 7.5 with BAG3, while the ER membrane sensor NFE2L1 falls; 11 of 13 significant heat shock protein genes are higher.

Limitations

  • Both AREE records from this study (the other is CGIG_HEAT24H_RNASEQ_PRJNA407831, 24 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