Abstract:

Total mRNA and miRNA profiles of 48 hpf red drum larvae after slick (1.25%, 2.5%, 5%) and source oil (0.135%, 0.27%, 0.54%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ. All mRNA reads were pooled and assembled de novo using Trinity. Known and novel miRNAs were identified using miRDeep2. Statistical bioinformatic analysis was further conducted by DAVID and Ingenuity Pathway Analysis to reveal dose-response biological effects of oil exposure.

Suggested Citation:

Xu, E.G., Esbaugh, A., Schlenk, D.. 2019. Dose-response RNA sequencing on red drum larvae after slick and source oil exposure. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-6avp-gw11

Publications:

Xu, E. G., Khursigara, A. J., Li, S., Esbaugh, A. J., Dasgupta, S., Volz, D. C., & Schlenk, D. (2019). mRNA-miRNA-Seq Reveals Neuro-Cardio Mechanisms of Crude Oil Toxicity in Red Drum (Sciaenops ocellatus). Environmental Science & Technology, 53(6), 3296–3305. doi:10.1021/acs.est.9b00150

Purpose:

To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, transcriptomic profiles in red drum embryos exposed to different concentrations of DWH oil were evaluated using High Throughput Sequencing (HTS).

Data Parameters and Units:

Sample infor.xlsx: GEO accession numbers for message and microRNA. RNA type, SampleName, Species, development stage, oil type, Tissue, Concentration, File type. Trinity.fasta: mRNA reads pooled and assembled de novo using Trinity. Annotated assembly.xls: annotated assembly of genes.

Methods:

Total mRNA and miRNA profiles of 48hpf red drum larvae after oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSeq500.

Instruments:

Illumina NextSeq500

Individual Files: