Abstract:
The dataset contains transcriptomic responses to oil, a pathogen (Vibrio anguillarum), or both in spleen and liver tissues from southern flounder (Paralichthys lethostigma). These data are publicly available at the National Center for Biotechnology Information (NCBI) under accession number GSE149905.
Suggested Citation:
Rodgers, Maria L. and Robert J. Griffitt. 2021. Liver and spleen RNAsequencing data from southern flounder exposed to oil, a pathogen, or both. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/G2TM8BGX
Purpose:
To evaluate transcriptomic responses in spleen and liver of southern flounder (Paralichthys lethostigma) exposed to oil, a pathogen, or both.
Data Parameters and Units:
The dataset includes an Excel file with RNA-sequencing (RNA-seq) data from southern flounder (Paralichthys lethostigma) organized into multiple worksheets for various experimental conditions and an Excel file containing accession numbers linked to experimental variables. The headers are: Parameters: Name (gene name), Log2 fold change (value), Fold change (value), P-value (value), FDR p-value (value), GEO Accession number, Treatment Day, Water temperature, pH, Dissolved oxygen (mg/L), Salinity (ppt), Total ammonia (mg/L), Oil (ug/L), sum PAH51, and V. anguillarum concentration (CFU/mL).
Methods:
Juvenile flounder (~90 days post-hatch) obtained from the University of Texas Marine Science Institute were maintained in flow-through tanks and fed brine shrimp nauplii and commercial fish food (Finfish silver, Zeigler® brand) twice per day prior to the experiment and held in water within 2°C of experimental tanks within 48 hours of experiment.
There were eight treatments: No Oil/No Pathogen Control 1, No Oil/No Pathogen Control 2, Low Oil/No Pathogen, High Oil/No Pathogen, No Oil/Pathogen 1, No Oil/Pathogen 2, Low Oil/Pathogen, and High Oil/Pathogen.
The exposures were performed in triplicate 10-gallon aquaria containing 2 kg/tank of sediment with 20 L of artificial seawater at a salinity of 15, and eight juvenile flounder. Each exposure tank received clean seawater at a rate of 666.7 mL/hour, which maintained optimal water quality parameters (temperature, pH, oxygen, ammonia, salinity).
After a seven-day oil exposure, the fish were removed from the exposure tank for a 1-hour bacterial challenge. Flounder assigned to control and Oil/No Pathogen challenge were placed into 10-gallon tanks containing 20 L of bacteria-free filtered seawater. Fish from No Oil/Pathogen challenge and Oil/Pathogen challenge treatments were placed into 10-gallon tanks with 20 L of filtered seawater containing 9.03 X 10^5 ± 5.09 X 10^4 cfu/mL V. anguillarum (ATCC strain 19264). After the 1-hour challenge, the flounder were returned to their respective exposure tanks for 48 hours. At 24 hours post-challenge, two fish were sacrificed from each tank. Liver, spleen, kidney, intestine and gill samples were removed, preserved in RNALater, and stored at -80°C until further processing.
To obtain a genome-wide view of the flounder transcriptome and gene expression profile following oil exposure, high-throughput RNA-seq was performed using Illumina sequencing technology. RNA was isolated from livers as discussed above and sequenced on an Illumina HiSeq2000.
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