CGIG_THERMOTOL_RNASEQ_PRJNA694496

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

F2 population after two generations of artificial selection using 42 C heat shock for 1 h; larvae sampled at ambient hatchery conditions

Control

F2 non-selected control population; larvae sampled at ambient hatchery conditions

Biological replication

RNA-seq: 3 selected-population and 3 control-population larval libraries; number of larvae pooled per library was not reported

Phenotype interpretation

Selected population had higher post-heat-shock survival (78.05% versus 66.34%) and field summer survival (73% versus 62%)

Analysis status

raw_reanalysis_harmonized

Quality control and results

All 132,413,989 read pairs quantified with Salmon 1.10.3; mapping rates 42.13-63.94%; PC1 explains 90.6% of variance and separates selected from control; selected_A is displaced on PC2 and has six genes above the Cook’s-distance threshold, but leave-one-out effects correlate 0.962 with the primary model and preserve the direction of all 8,802 primary significant genes

Limitations

  • The RNA-seq comparison is constitutive selected-versus-control expression at the larval stage, not an acute heat-versus-control contrast.
  • Thermotolerance survival was measured in related later-stage cohorts rather than the RNA-sequenced larval pools.
  • The publication reports 4,764 DEGs but does not provide the complete feature-level effect, p-value, or standard-error table in its supplementary archive.
  • The publication describes three replicates per group but does not report how many larvae were pooled into each RNA-seq library.
  • All six runs share one BioSample record, and its tissue field says gill despite the publication consistently describing whole umbo larvae; AREE follows the publication for tissue and records the discrepancy.
  • The source genome assembly and differential-expression software/threshold are not reported clearly enough for exact reproduction; AREE used GCF_963853765.1/RS_2024_06, so these results are a current-reference reanalysis rather than an exact reconstruction of the publication pipeline.
  • Selected_B and selected_C have lower Salmon mapping rates than the other libraries, and selected_A is displaced on PC2; sensitivity analysis supports the primary effect directions, but these patterns remain QC caveats.

Sources