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Supplemental Information

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.

DOI: 10.7287/peerj.preprints.2977v1/supp-1

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.

DOI: 10.7287/peerj.preprints.2977v1/supp-2

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.

DOI: 10.7287/peerj.preprints.2977v1/supp-3

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.

DOI: 10.7287/peerj.preprints.2977v1/supp-4

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.

DOI: 10.7287/peerj.preprints.2977v1/supp-5

Additional Information

Competing Interests

Keith A. Crandall is an Academic Editor for PeerJ.

Author Contributions

Hernan Vazquez-Miranda performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Brent P Thoma conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Juliet M Wong performed the experiments, reviewed drafts of the paper.

Darryl L Felder conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Keith A Crandall conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Heather D Bracken-Grissom conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

Annotated transcriptome assembly and additional data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org/data/R4.x257.228:0013. (DOI: http://dx.doi.org/10.7266/N71C1TZC). The raw data used in this study is available at the NCBI website under BioProject ID: PRJNA376168 (https://www.ncbi.nlm.nih.gov/bioproject/376168), BioSamples SAMN06351232-SAMN06351246. Transcriptome Shotgun Assembly (TSA) has been deposited at DDBJ/EMBL/GenBank under the accession GFJG00000000 (version 1.0: GFJG01000000). TSA file prepared with Transvestigator at http://doi.org/10.5281/zenodo.10471

Funding

This research was made possible in part by a grant from The Gulf of Mexico Research Initiative, and in part by Florida International University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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