Abstract:

The dataset contains transcriptomic responses to oil, a pathogen (Vibrio anguillarum), or both in spleen and liver tissues from two different fish species - juvenile Atlantic croaker (Micropogonias undulatus) and red drum (Sciaenops ocellatus). These data are publicly available at the National Center for Biotechnology Information (NCBI) under accession numbers GSE135979 (Atlantic croaker) and GSE136133 (red drum) respectively.

Suggested Citation:

Robert J. Griffitt, Maria L. Rodgers. 2019. RNA-sequencing data from Atlantic croaker (Micropogonias undulatus) and red drum (Sciaenops ocellatus). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-47hg-z293

Purpose:

These data were generated in order to gain a better understanding of how oil alone, a pathogen alone, and both stressors together influence the transcriptome of various commercially and recreationally important fish species.

Data Parameters and Units:

The dataset includes an excel file with RNA-sequencing (RNA-seq) data from Atlantic croaker (Micropogonias undulatus) and red drum (Sciaenops ocellatus) organized in the multiple worksheets for various experimental conditions. Parameters: Name (gene name), Log2 fold change (value), Fold change (value), P-value (value).

Methods:

High-energy water accommodated fraction (HEWAF) stock solution was prepared using the method for large volume HEWAF production described by Forth et al., (2016), with modifications. Un-weathered, source oil collected from the Deepwater Horizon (DWH) riser was used in the preparation of the stock HEWAF solution with a nominal concentration of 1 g/L. HEWAF was prepared using a heavy-duty blender (Waring Commercial). Three liters of artificial seawater were combined with 3.6 mL of source oil in a 3.8 L stainless steel blender container. The water-oil mixture was mixed on the low setting for 30 seconds and transferred to a 4 L separatory funnel. The separatory funnel containing the HEWAF solution was covered with aluminum foil, and allowed to settle for 1 hour. Following the 1 hour settling period, the HEWAF stock solution was used to prepare experiment treatment concentrations by dilution. The pathogen was being evaluated for Vibrio anguillarum that was obtained from ATCC (19264) and grown to the targeted nominal density of 2.65*108 CFU/mL in marine broth. Fish were challenged for one hour. Some fish were control (no oil/no pathogen), some were oil only, some were pathogen only, and some were oil+pathogen. All fish were all aquaculture-reared.

Provenance and Historical References:

Forth, H. P., Mitchelmore, C. L., Morris, J. M., & Lipton, J. (2016). Characterization of oil and water accommodated fractions used to conduct aquatic toxicity testing in support of the Deepwater Horizon oil spill natural resource damage assessment. Environmental Toxicology and Chemistry, 36(6), 1450–1459. doi:10.1002/etc.3672

Individual Files: