Abstract:
This dataset contains gene expression profiles from RNA sequence data of corals at sites impacted by the Deepwater Horizon oil spill and a reference site. Specifically, Paramuricea biscaya colonies were collected in November and December of 2010. This dataset supports the publication, DeLeo, D.M.; Herrera, S.; Lengyel, S.D.; Quattrini, A.M.; Kulathinal, R.J.; Cordes, E.E. (2018). Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill. Molecular Ecology, 27, 20, 4066-4077. doi:10.1111/mec.14847
Suggested Citation:
Danielle DeLeo. 2018. Dataset for: Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N75H7DWD
Data Parameters and Units:
Supplemental_annotation_table_S1.xlsx: Genes significantly differentially expressed in spill-impacted Paramuricea biscaya colonies (exp685 and exp686) relative to control colonies (unexp43 and unexp47). Contains log2-fold changes for genes over- (positive) and under- (negative) expressed in impacted colonies, respective count values for each coral colony and the corresponding best-hit BLAST, Gene Ontology (GO) and pfam annotations. Differential gene expression was considered significant if adjusted p-values (FDR) < 0.05 and absolute log2 fold-change (FC) was >1. Transcripts are sorted and color-coded based on corresponding clusters (hierarchical clustering using Pearson correlation-based distances). Red-coded genes are significantly over-expressed in both impacted corals, relative to controls, to a similar degree. Blue coded genes are also over-expressed among impacted corals, but to a higher degree in impact colony-exp686, and to a lesser extent in colony-exp685, and vice versa for the green-coded genes. Yellow and pink coded gene clusters were significantly under-expressed in both impacted corals.
Transcript ID: identifier for that particular sequence in the reference assembly, that can be cross referenced to the annotation report.
Trinity transcript ID: unique identifier assigned to contigs assembled by trinity and sequence isoforms. This can also be cross referenced between the assembled contigs and the annotation report.
Pbiscaya_RNAseq_metadata.xlsx: RNAseq_Specimens worksheet: Sample_ID, Site, Latitude (decimal degrees), Longitude (decimal degrees), Date, Species, Depth (m), SRA_accession, SRA_study_ID, BioProject_ID, BioSample_ID. Transciptome_assembly worksheet: Number of transcripts, Mean length base pairs (bp), Reconstruction size (bases), Transcripts over 1k bp, Transcripts over 10k bp, Transcripts with open-reading frames (ORFs), GC content, N50 (bp), Transrate score.
Note that the coordinates for exp686 and unexp47 are incorrect in the data file. The coordinates for the samples are:
exp685 MC294 28.6722 −88.4765
exp686 MC294 28.6722 −88.4766
unexp43 MC344 28.6337 −88.1698
unexp47 MC344 28.6337 −88.1699
Methods:
Samples were preserved in RNAlater in situ. Total RNA was extracted using a Qiagen RNeasy Kit or a modified Trizol/Qiagen RNeasy protocol (described in Burge et al. 2013, Polato et al. 2010) in cases where tissue was limited. mRNA library preparation (TruSeq RNA Library Preparation Kit v2) and high-throughput Illumina sequencing (HiSeq2000; 100 base pair (bp), paired-end reads) was conducted at the University of Wisconsin-Madison Biotechnology Center (UWBC, Madison, WI).
Provenance and Historical References:
Burge, C. A., Mouchka, M. E., Harvell, C. D., & Roberts, S. (2013). Immune response of the caribbean sea fan, Gorgonia ventalina, exposed to an aplanochytrium parasite as revealed by transcriptome sequencing. Frontiers in Physiology 4, 1–9. doi:10.3389/fphys.2013.00180
Polato, N.R., Voolstra, C.R., Schnetzer, J., DeSalvo, M.K., Randall, C.J., Szmant, A.M., Medina, M. and Baums, I.B. (2010). Location-Specific Responses to Thermal Stress in Larvae of the Reef-Building Coral Montastraea faveolata. PLoS ONE, 5(6), e11221. doi:10.1371/journal.pone.0011221
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