Abstract:

Illumina high-throughput RNA-sequencing technology was used to sequence, assemble and annotate the transcriptome of tissues from southern flounder exposed to Louisiana crude oil. This dataset contains SRA accession numbers for RNA sequencing data located at the National Center for Biotechnology Information, log2 fold change, annotated assembly, and fasta files.

Suggested Citation:

Dana Wetzel, Tracy Sherwood, and Rebecca Medvecky. 2019. RNA-seq transcriptome characterization of tissue from sub-adult southern flounder exposed to Louisiana crude oil contaminated sediment. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-58ge-3329

Purpose:

Controlled oil exposure study to evaluate the effects of south Louisiana crude oil, via contaminated sediment, on fish health.

Data Parameters and Units:

Test 211 RNAseq R4.x267.000:0072.xlsx file contains the following worksheets: Tank Description worksheet: Tank ID, Sediment Start date, Fish Added date, Treatment, Number of Fish. Sediment Preparation worksheet: Date, Time, Tank, Oil (g), Oil ID, Sediment (kg). Test 211 Sample Key worksheet: Collected date, Field ID, Treatment, Matrix, MML Number, Species, Gender, Weight (g), Length (cm). Sample Accession Numbers worksheet: biosample_accession, accession, MML Number, Organism, Dev_stage, sex, matrix, collection_date, treatment. Gene_exp.diff.xlsx: test_id, gene_id, gene, locus, sample_1, sample_2, status, value_1, value_2, log2(fold_change), test_stat, p_value, q_value, significant (yes, no). Trinotate_annotation_report.xls: annotated assembly of genes. RNA sequences in fasta files: transcripts.fasta and tss_yellow_highlighted.fasta

Methods:

log2Fold change in gene expression, using Paralichthys olivaceus (Japanese flounder) RefSEq assembly: GCF_001970005.1 as reference sequence for mapping of the reads.

Individual Files: