CGIG_PESTO_F1PARENTAL_RNASEQ_PRJEB58194

Primary-analysis sample count: 12. The counted unit and independent experimental units are described under Biological replication; counts may represent animals, pools or libraries.

Treatment

Unexposed F1 offspring of parents that were exposed to the pesticide mixture during their own embryo-larval development (ET); sampled as gastrulae (6 hpf) and metamorphosis-competent pediveligers

Control

F1 offspring of control parents, unexposed (TT)

Biological replication

12 libraries: 6 TT and 6 ET, three per stage.

Phenotype interpretation

The publication found that parental exposure drove the offspring phenotype more than direct exposure: offspring of exposed parents had lower epinephrine-induced metamorphosis and field survival, and RNA-seq and methyl-seq separated offspring by F0 treatment. AREE records the intergenerational transcriptional effect averaged over two stages.

Analysis status

raw_reanalysis_complete_not_harmonized

Quality control and results

All 12 libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 42.0% in TT and 43.8% in ET pools on average. Expressed-SNP allele frequencies at 295 sites show ET and TT pools are genetically distinct: they differ 3.6 times more than pools of one group (excess over same-RNA noise 0.058 against 0.016 at the same stage), because offspring of exposed and of control F0 parents necessarily have different parents. ~ stage + condition (6 v 6) gives 307 of 24,153 genes at FDR < 0.05, led by CD109 antigen-like genes (log2FC -5 to -6) whose very large changes are typical of lineage presence-absence variation, so parental exposure cannot be separated from parentage and the record is not harmonized.

Limitations

  • The two F1 records (direct exposure TE and parental exposure ET) test against the same six TT libraries, so they carry the dependence group PRJEB58194_F1_TT and count as one replication group.
  • The contrast compares offspring of different parents, so a parental-exposure effect can be confounded with parentage; the expressed-SNP check measures the genetic distance between the ET and TT pools.
  • The exposure is a mixture of 18 pesticides and metals at environmentally relevant concentration (nominal sum 2.85 ug/L; measured 3.74 ug/L in F0) during embryo-larval development (0-48 h post fertilization) at the Ifremer Bouin hatchery.
  • Each library is presumably a pool of many embryos or larvae; pool size, culture vessels and the meaning of the F0 group digits (1-3) are not recorded in the public metadata, and pools were checked with the expressed-SNP test (scripts/check_replicate_genotypes.py) before analysis.
  • All runs come from NCBI .sra archives checked against NCBI’s MD5s (11 F0 runs have no ENA FASTQ), with read counts checked against the NCBI spot counts on conversion.
  • The study also deposited F0 pediveligers (sampled after exposure) and F1 offspring exposed in both generations (EE); AREE does not use them.
  • Not harmonized into the evidence base (decision 2026-10-09): the parental-exposure contrast is confounded with parentage (ET and TT pools differ genetically 3.6 times more than pools within a group), as in CGIG_OA_RNASEQ_PRJNA1196326. The DESeq2 results are kept outside the repository.

Sources