CGIG_PESTO_F0_RNASEQ_PRJEB58194

Primary-analysis sample count: 36. The counted unit and independent experimental units are described under Biological replication; counts may represent animals, pools or libraries.

Treatment

Exposed to the pesticide mixture from 0 to 48 h post fertilization; sampled as gastrulae (6 hpf) and D larvae

Control

Unexposed F0 gastrulae and D larvae from the same hatchery cohort

Biological replication

36 libraries: 18 control and 18 exposed, nine per stage (gastrula, D larva), labelled with group digits 1-3 and replicate letters A-F.

Phenotype interpretation

The publication found no difference in embryo-larval abnormalities at 24 hpf, disturbed swimming, larger and heavier exposed larvae at some times, a lower epinephrine-induced metamorphosis rate and higher field survival, and differential expression of developmental genes (Hox orthologues, cell-cycle regulators) in gastrulae. AREE records the transcriptional response averaged over two stages.

Analysis status

raw_reanalysis_harmonized

Quality control and results

All 36 F0 libraries quantified with Salmon 2.3.4 against GCF_963853765.1/RS_2024_06 from NCBI .sra archives that match NCBI’s MD5s; mapping 52.8% in controls and 50.3% in exposed pools on average (31.7-65.6% across the 54 PESTO libraries). Expressed-SNP allele frequencies at 460 sites show the F0 pools come from one cohort: control and exposed pools at the same stage differ no more than pools of one treatment (excess over same-RNA noise 0.0165 against 0.0158), so exposure is not confounded with parentage, and no pair is resequenced RNA; the two runs sharing the title BT2Ed are different pools (excess 0.0138). Allele frequencies diverge more between stages (excess 0.032), as in other larval studies. PC1 (96%) is developmental stage. ~ stage + condition (18 v 18): 644 of 21,104 tested genes reach FDR < 0.05 (255 higher, 389 lower with the mixture); adding the F0 group digit as a block gives 642 (566 shared, 643 of 644 same direction, log2FC r = 0.905). Three group-3 control D larvae are the least correlated libraries, a group effect absorbed by that sensitivity model. The response includes five homeobox genes (engrailed-1-B lower), M-phase inducer phosphatase (cdc25) higher and seven cytochrome P450 genes lower, matching the publication’s development-related genes (Hox orthologues, cell-cycle regulators).

Limitations

  • One control D-larva sample title (BT2Ed) is attached to two runs (ERR10659105, ERR10659106); both are kept with the run accession appended to the replicate, and the expressed-SNP check tests whether they are one sample.
  • 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