Abstract:

To investigate the methylation altering effects of oil and hypoxia on developing fish, larval Cyprinodon variegatus was exposed to oil, hypoxia, or both for 48 hours followed by 48 hours of depuration. Immunoprecipitation coupled with high-throughput sequencing (MeDIP-seq) was used to evaluate genome-wide methylation changes. Additionally, RNA-seq was performed on samples from this experiment to determine the relationship between changes in DNA methylation and transcriptional profiles.

Suggested Citation:

Jones, Elizabeth R.. 2021. DNA methylation and transcription data profiles in larval fish Cyprinodon variegatus exposed to oil, hypoxia, or both. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/9V817G79

Purpose:

This data documents genome-wide methylation changes following oil exposure. It also allows comparison of DNA methylation and transcriptional patterns to determine the extent of methylation-modulated gene expression following oil and hypoxia exposure.

Data Parameters and Units:

The headers are Sample, Tissue (whole body; n = 5 larvae), Molecule (ssDNA/ total RNA), Organism (Cyprinodon variegatus), Age (8 days post-hatch/ 6 days post-hatch), tPAH50 (µg/L), Oxygen (mg/ml), Salinity and GEO Accession number.

Methods:

C. variegatus brood stock were maintained at the University of Southern Mississippi’s Toxicology Lab in Ocean Springs, MS. Fish were kept in 300 L circulating raceways containing 15 ppt artificial sea water at 25°C and 15 ppt salinity on a 16:8 light/dark cycle and fed commercial flake food daily. Breeding was initiated by the placement of breeding nets in raceways. After 12 hours embryos were collected and examined for fertilization. Embryos were rolled on mesh mats to remove external villi, and incubated in 15 ppt sea water at 30°C with agitation to prevent clumping. After hatching, embryos were reared until yolk-sacks were absorbed and larvae began free-feeding (4 days post-hatch). Upon initiation of feeding, larvae were fed Artemia nauplii once daily. Feeding continued throughout experiments. For MeDIP sequencing: Bases Called using Illumina HiSeq Control Software. Initial processing of data was performed using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany). Adaptor sequences and low quality reads were trimmed, paired ends matched, and reads aligned to the C. variegatus genome. Differentially methylated regions were identified using the MEDIPS R package (v 1.34). To calculate differential methylation, the C. variegatus genome was divided into consecutive 100 bp windows, and read depth for each window compared between control and treatment samples. For RNA sequencing: Bases Called using Illumina HiSeq Control Software. Initial processing of data was performed using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany). Adaptor sequences and low quality reads were trimmed, paired ends matched, and reads aligned to the C. variegatus genome. Reads were aligned to C. variegatus genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany). Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany). The oil used to prepare HEWAF for these experiments was Slick A (oil obtained on July 29, 2010 from the hold of barge number CTC02404, which received surface slick oil from multiple skimming vessels operating near the Macondo Well).

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