Abstract:

This dataset contains the raw reads generated from RNA sequencing of the transcriptome of liver tissue collected from controls (three replicates) and chemically enhanced water accommodated fraction (CEWAF, three replicates) exposed red drum (Sciaenops ocellatus). Illumina high-throughput RNA-sequencing technology was used to sequence, assemble and annotate the transcriptome of tissues from livers of the red drum after exposure to CEWAF/Control. This dataset is available at the NCBI-SRA database accession number SRP159002.

Suggested Citation:

Dana Wetzel, Tracy Sherwood, Christelle Miller and Rebecca Medvecky. 2019. Red drum CEWAF uptake/depuration study: RNA-seq transcriptome characterization of tissue. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N78P5Z08

Purpose:

This study was done to determine any sub-lethal effects of dispersed oil (CEWAF) exposure to juvenile red drum.

Data Parameters and Units:

The worksheet “Test Conditions table” contains information regarding the setup of the experiments in terms of species, life stage of species, exposure type, renewal frequency, number of replicates per treatment, description of treatments. The worksheet “Tank Descriptions”: Tank ID (identifier); Start date (MM/DD/YYYY); End date (MM/DD/YYYY); Treatment (Control/CEWAF); Number of fish; Notes; Recorded by. The worksheet “CEWAF Prep”: Date (date when CEWAF was made; MM/DD/YYYY), Carboy ID, Oil (the amount of oil added to the mixture; g); Corexit (the amount of Corexit added to the mixture; g); Volume Water (quantity of water; L). The worksheet “Test 113 Sample Key”: Day (day of fish harvest); Sample Date (time of sampling; MM/DD/YYYY); Sample Location (MAP - Mote Aquaculture Program); Tank ID (identifier); Matrix (organ that was tested; liver); MML # (identifier); and Treatment (control or CEWAF). The file "Test 113 NCBI_metadata-RNAseq_SRP159002 R4.x267.0000066.xlsx": Accession (identifier for submission to NCBI for a sequence); study” (identifier of the study); object_status; bioproject_accession (identifier for project); biosample_accession (identifier for a biosample); sample_name (identifier for sample); library_ID (identifier for library identification); title; library_strategy ( sequencing technique); library_source (source material to be sequenced); library_selection (the means by which the material being sequence is selected); library_layout (whether to expect single or paired-end reads); platform; instrument_model; design_description (a brief narration on how library was prepared); filetype; assembly; and filename.

Methods:

Experimental Treatment Information: There were two treatments - Control and 1ppm CEWAF. The test was 24-hour CEWAF renewal, flow-through exposure for 4 days, followed by six days of clean seawater. The control was a constant flow of clean seawater during the exposure period. Each tank started with 20 fish. Two fish were sampled from each tank on days 1-4 and days 6, 8, and 10. Remaining fish were moved to grow-out tanks of clean seawater and sampled at the 90-day mark. Livers were aseptically dissected from the juvenile red drum, euthanized using MS‌-222 at 300 ppm for 15 minutes. At sacrifice, the livers of two fish from each tank were rinsed with PBS and a 5mm3 portion of each liver was placed immediately in RNAlater™ (Sigma-Aldrich Corp., USA), the remainder of the livers were placed in a glass container and stored at -20ᵒC until ∑50PAH analysis. Total RNA was extracted from 30 mg of each tissue using Tri-Reagent® (Sigma-Aldrich Corp., USA) following the manufacturer’s instructions. RNA quantity was evaluated by the Qubit 3.0 Fluorometer (Life Technologies, USA) and quality with the ND‌-2000 (Nanodrop Technologies) and 2100 Bioanalyzer (Agilent, USA). One mg of total RNA from each pair of liver samples was sent for RNA sequencing.

Individual Files: