Table S1. Sample information.
Specimen voucher number (HBG) deposited at Florida International University, locality, experimental treatment, Genbank BioSample accession, and number of pair-end reads obtain per stranded RNAseq HiSeq2000 Illumina library. Experimental conditions were: aerated, negative control (AC), non-aerated, negative control (NC), non-aerated treatment with oil (WAF; OO), and non-aerated treatment with oil mixed with dispersant (CEWAF; OD). The letter ‘R’ represents the individual replicate number. Reference treatments were used exclusively for the de novo transcriptome assembly.
Table S2. Pairwise counts of differentially expressed features between aerated and non-aerated experimental treatments.
Numbers represent transcripts with significant differential expression in a log2 fold change scale after passing an FDR of 1% in edgeR and DEseq2. Each treatment included three replicates. Experimental conditions were: aerated, negative control (AC) and non-aerated, negative control (NC). These comparisons exclude non-aerated treatments with oil and dispersant (OO and OD) to determine transcripts expressed in hypoxic conditions.
Table S3. Pairwise counts of differentially expressed features between non-aerated experimental treatments with and without oil and dispersant.
Numbers represent transcripts with significant differential expression in a log2 fold change scale after passing an FDR of 1% in edgeR and DESeq2. Each treatment included three replicates. Experimental conditions were: non-aerated, negative control (NC), non-aerated oil-only treatment (WAF; OO), and non-aerated oil-dispersant treatment (CEWAF; OD). These comparisons exclude the aerated, negative control (AC) to avoid masking the effects of experimental manipulation and low oxygen in expressed transcripts.
Table S4. Gene ontology and gene regulation direction.
These gene ontology terms were detected by both statistical methods for Trinity genes and isoforms and are listed in alphabetical order following the oil-dispersant treatment (OD) directionality. Left column correspond to the list number, central column to the gene ontology term for downregulated features, and right column corresponds to upregulated features. The non-aerated, negative control (NC) replicates had the inverse regulation directionality.
Table S5. Tumor necrosis factor (TNF) and Cytochrome P450 (CYP) downregulated transcripts.
(3 and 19 total respectively) in the oil-dispersant treatment (OD) detected by DESeq2 (and thus upregulated in the negative control). These features were not detected by edgeR. Transcripts blasted to the same GO molecular functions, for TNF: receptor binding, and for CYP: Heme binding, iron ion binding, monooxygenase activity, and oxydoreductase activity. Organism Uniprot identity: Kuruma prawn – PENJP (Penaeus japonicus), fruit fly - DROME (Drosophila melanogaster), house mouse - MOUSE (Mus musculus), and tropical cockroach - BLADI (Blaberus discoidalis). For full annotations see DS1, and DS4-5.