{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Fekadu Yadetie"],"organism":["Gadus morhua"],"software":["Illumina NovaSeq 6000 System"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16384"],"description":["This study investigates how parental exposure to the water-soluble fraction (WSF) of crude oil influences transcriptomic profiles in Atlantic cod (Gadus morhua) offspring. Fish were exposed to WSF for 20 days prior to spawning, and four offspring groups were generated by fertilization: control (unexposed parents), maternally exposed, paternally exposed, and biparentally exposed. Transcriptome analyses of embryos were performed at key developmental stages at 0, 2, 4 and 21 days post feralization (dpf) and the observed changes were correlated with phenotypic traits such as cardiac function and morphological measurements.  Offspring groups from exposed females died before hatching. Transcriptome analyses indicated severe suppression or absence of expression of genes involved in early development in the maternally exposed groups. In contrast, paternal exposure had minimal impact on gene expression, and no phenotypic abnormalities were observed at hatching. Nonetheless, reduced survival in early larval stages suggested sublethal toxicity of crude oil."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - Spawning 4-year-old Atlantic cod (Gadus morhua) (n = 40) obtained from Nofima (Nofima AS, Kraknes, Norway) were divided into unexposed control group (11 females, 9 males) and an oil-exposed group (12 females, 8 males), and kept in 3000 L flow-through tanks at Tromsø Aquaculture Research Station (Kårvik), supplied with filtered seawater under a natural photoperiod (latitude 69° N).    Exposure to a WSF of Goliat (Kobbe) crude oil (Vår Energi) was performed using an oiled gravel column system adapted from Carls et al. (1999). Exposure (for 20 days) was started on February 19, at the final stages of gonadal maturation and terminated when fish in the exposed group exhibited loss of equilibrium and mortality was observed.     Gamete pools and in vitro fertilization for offspring groups: Strip-spawning was initiated on March 10, after natural spawning activity was observed in both control and exposure tanks. Gametes were collected and fertilized in vitro on March 26. Eggs from the five females with the largest volumes of stripped oocytes in each group were pooled for the cross-fertilization, along with sperm from all males in the respective groups. Fertilization was set up to generate four distinct offspring groups: Control (P1), from non-exposed parents, maternally exposed (P2), paternally exposed (P3), and biparentally exposed (P4).   Fertilization was performed by gently mixing 565 mL of the oocyte pool with 3 mL of the sperm pool. Followed by addition of 1 L of clean facility water for sperm activation. After incubating the mixture for 10 minutes, the eggs were carefully rinsed with clean facility water using a sieve before being transferred to a 25 L flow-through incubator equipped with an airstone. Fertilization for all offspring groups was completed within 60 minutes. At 1 dpf, all buoyant eggs were collected with a fine mesh net and evenly divided into 25 L replicate flow-through incubators (n= 5 per treatment) and kept under a natural light regime (latitude 69 °N) and ambient seawater temperatures (mean 4.4 °C)  until 23 dpf (2 days post hatch (dph)). Maternally exposed groups (P2 and P4) died by 7 dpf, and only the control (P1) and paternal (P3) offspring groups were left for the rest of the experiment. Hatching reached 50 % at 21 dpf (0 dph). At 23 dpf (2 dph), all larvae were transferred to 190 L flow-through feeding tanks and fed with green water and rotifers daily until 33 dpf, and then exclusively with rotifers. The water temperature was gradually increased over the rearing period from 5.4 to 10.1 °C. The experiment was terminated at 42 dpf (21 dph), when three out of the five replicate tanks of the paternally exposed group showed 100 % mortality.","Sample Collection - At 1 dpf, embryos (approx. 50) were sampled from the water surface of each replicate incubator for egg diameter measurements. Embryos (approx. 100 per timepoint) for transcriptome analysis were collected from the water surface of each incubator and immediately snap-frozen in liquid nitrogen before storage at -80 °C. Sampling timepoints were selected to cover major developmental periods: fertilization (0 dpf), blastula period (2 dpf), gastrulation (4 dpf), segmentation (10 dpf) and hatching (21 dpf).","Sequencing - Sequenced by Novogene on Illumina NovaSeq 6000 System","Growth Protocol - Spawning 4-year-old Atlantic cod (Gadus morhua) (n = 40) obtained from Nofima (Nofima AS, Kraknes, Norway) were divided into unexposed control group (11 females, 9 males) and an oil-exposed group (12 females, 8 males), and kept in 3000 L flow-through tanks at Tromsø Aquaculture Research Station (Kårvik), supplied with filtered seawater under a natural photoperiod (latitude 69° N).","Nucleic Acid Extraction - Samples were homogenized with a mortar and pestle on dry ice and total RNA extraction was performed using TRIzol Reagent (Invitrogen, USA) following the manufacturer’s protocol. RNA quality and concentration were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All samples demonstrated high RNA integrity, with RNA Integrity Number (RIN) ≥ 8.8.","Library Construction - Sequenced by Novogene on Illumina NovaSeq 6000 System"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Using DESeq2 (Anders and Huber 2010; Love et al. 2014)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Understanding the long-term biological consequences of crude oil exposure on marine fish is essential for the sustainability of ecologically and economically important species such as Atlantic cod (Gadus morhua). While the direct effects of crude oil on early life stages are well documented, adult reproductive vulnerability and intergenerational consequences remain poorly understood, despite their pivotal role in spawning stock viability. Paternal contributions to next-generation outcomes are particularly underexplored. This study examined how parental exposure to a water-soluble fraction of crude oil affects transcriptomic profiles and survival outcomes in Atlantic cod offspring. Adult fish were exposed for 20 days prior to spawning, and offspring were produced by in vitro cross-fertilization to generate four groups: control (unexposed parents), maternally exposed, paternally exposed and biparentally exposed. Embryos were reared under control conditions, and transcriptome profiles were analyzed from fertilization to hatching, alongside assessments of cardiac function and morphology post-hatch. Offspring from exposed females failed to survive to hatching. Eggs were smaller, and transcriptomic data revealed severe downregulation of genes involved in early developmental processes. Chemical analyses confirmed maternal transfer of a diverse range of petroleum aromatic hydrocarbons to oocytes. Our findings point to disrupted oocyte provisioning, likely linked to endocrine and epigenetic disturbances during oocyte maturation. Paternal exposure had minimal effect on RNA expression, and morphology at hatching. However, reduced survival in early larval stages suggests sublethal effects emerging later, possibly through epigenetic mechanisms, a hypothesis requiring further investigation."],"study_type":["RNA-seq of coding RNA"],"species":["Gadus morhua"],"pubmed_title":["Maternal and paternal crude oil exposure differentially shapes early developmental transcriptomes and survival outcomes in Atlantic cod (Gadus morhua)."],"pubmed_authors":["Fekadu Yadetie","Claudia Erhart","Bjørn Henrik Hansen","Erhart C, Nahrgang J, Odei DK, Frantzen M, Sørensen L, Creese ME, Puvanendran V, Hansen ØJ, Hansen BH, Meador JP, Yadetie F.","Lisbet Sørensen","James P. Meador","Jasmine Nahrgang","Øyvind Johannes Hansen","Mari Egeness Creese","Derrick Kwame Odei","Marianne Frantzen","Velmurugu Puvanendran"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic effect of parental exposure to a crude oil water-soluble fraction in Atlantic cod (Gadus morhua) early life stages","description":"This study investigates how parental exposure to the water-soluble fraction (WSF) of crude oil influences transcriptomic profiles in Atlantic cod (Gadus morhua) offspring. Fish were exposed to WSF for 20 days prior to spawning, and four offspring groups were generated by fertilization: control (unexposed parents), maternally exposed, paternally exposed, and biparentally exposed. Transcriptome analyses of embryos were performed at key developmental stages at 0, 2, 4 and 21 days post feralization (dpf) and the observed changes were correlated with phenotypic traits such as cardiac function and morphological measurements.  Offspring groups from exposed females died before hatching. Transcriptome analyses indicated severe suppression or absence of expression of genes involved in early development in the maternally exposed groups. In contrast, paternal exposure had minimal impact on gene expression, and no phenotypic abnormalities were observed at hatching. Nonetheless, reduced survival in early larval stages suggested sublethal toxicity of crude oil.","dates":{"release":"2026-02-16T00:00:00Z","modification":"2026-05-27T16:40:24.869Z","creation":"2025-12-05T15:59:25.638Z"},"accession":"E-MTAB-16384","cross_references":{"pubmed":["41671699"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"],"doi":["10.1016/j.marpolbul.2026.119374"]}}