CGIG_PESTO_F1DIRECT_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

F1 offspring of control parents exposed to the pesticide mixture from 0 to 48 h post fertilization (TE); 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 TE, three per stage.

Phenotype interpretation

The publication found that the parents’ exposure shaped the offspring phenotype more than direct exposure did; offspring of exposed parents had lower epinephrine-induced metamorphosis and field survival. AREE records the transcriptional response to direct exposure averaged over two stages.

Analysis status

raw_reanalysis_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 47.2% in TE pools on average. Expressed-SNP allele frequencies at 310 sites show TE and TT pools are genetically equivalent (excess over same-RNA noise 0.0131 between against 0.0144 within, same stage), as expected for offspring of the same parents, with no resequenced RNA. PC1 (99%) is developmental stage. ~ stage + condition (6 v 6): 17 of 24,306 tested genes reach FDR < 0.05 (1 higher, 16 lower with direct exposure), a near-null response that agrees with the publication’s finding that direct exposure affects the F1 phenotype less than parental exposure.

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; only the direct-exposure record is harmonized.
  • 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.

Sources