Abstract:

Total mRNA profiles of 24, 48, 96 hours post fertilization mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25, and resulted in a Trinity_fasta.txt file.

Suggested Citation:

Xu, Elvis Genbo. 2017. De novo transcriptome of Mahi-mahi embryos. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7MW2F6S

Publications:

Xu, E. G., Mager, E. M., Grosell, M., Hazard, E. S., Hardiman, G., & Schlenk, D. (2017). Novel transcriptome assembly and comparative toxicity pathway analysis in mahi-mahi (Coryphaena hippurus) embryos and larvae exposed to Deepwater Horizon oil. Scientific Reports, 7, 44546. doi:10.1038/srep44546

Purpose:

To provide molecular resources for facilitating further investigations on the holistic understanding of the developmental toxicity of DWH oil in mahi-mahi.

Data Parameters and Units:

trinity_fasta.txt: mRNA profiles pooled and assembled with Trinity (k-mer lenth set at 25) sample infor.csv: GEO accession number, sample number, status, note, species, age, concentration (ng/ul) Trinotate.xls: #gene_id, transcript_id, sprot_Top_BLASTX_hit, TrEMBL_Top_BLASTX_hit, RNAMMER, prot_id, prot_coords, sprot_Top_BLASTP_hit, TrEMBL_Top_BLASTP_hit, Pfam, SignalP, TmHMM, eggnog, gene_ontology_blast, gene_ontology_pfam, transcript, peptide

Methods:

Total mRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25, and resulted a Trinity_fasta.txt file.

Instruments:

Illumina HiSeq2500, Biocluster

Provenance and Historical References:

GEO Accession Number: GSE79675

Individual Files: