Dataset for: Effects of Corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus)

Relationship of Effects of Cardiac Outcomes in Fish for Validation of Ecological Risk II (RECOVER II)

DOI:
10.7266/n7-sfa3-9041
 
UDI:
R6.x804.000:0029
Last Update:
Jul 11 2019 17:02 UTC
 
Dataset Author(s):
Greer, J.
Point of Contact:
Schlenk, Daniel
University of California Riverside / Department of Environmental Sciences
900 University Avenue Geology 2258
Riverside, California  92521
USA
daniel.schlenk@ucr.edu
Funding Source:
RFP-VI
 
Extent Description:
Dataset contains laboratory measurements of transcriptomic responses, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Greer, J.. 2019. Dataset for: Effects of Corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-sfa3-9041

Abstract:

The goal of this project is to better understand the combined effects of oil and dispersant that larvae were likely exposed to after the spill. Mahi larvae will be exposed to varying sublethal concentrations of both Corexit alone and Corexit combined with slick oil. Transcriptional responses will be assessed using RNASeq after 48 hours of exposure. Thus this dataset consists of measurements of polycyclic aromatic hydrocarbons and dioctyl sodium sulfosuccinate (DOSS), videos of heart rate of mahi-mahi (Coryphaena hippurus) larva, phenotype images and larval RNA sequences. This dataset supports the publication: Greer, J. B., Pasparakis, C., Stieglitz, J. D., Benetti, D., Grosell, M., & Schlenk, D. (2019). Effects of corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus). Aquatic Toxicology, 212, 233–240. doi:10.1016/j.aquatox.2019.05.014

Purpose:

To further understand the toxicity of Corexit and Corexit-oil mixtures on early life stage mahi-mahi.

Theme Keywords:

mahi-mahi, cardiac development, transcriptomics, corexit, dispersant, chemical dispersion, Chemically-enhanced water-accommodated fractions (CEWAFs), Coryphaena hippurus, Polyaromatic hydrocarbon, Developmental toxicity, Gene expression

File Format:

mov, jpg, xls, xlsx, txt, fasta

Filename:

R6x8040000029 transcriptional responses mahi corexit oil.zip (521.24 MB)

Dataset Downloads:

1

Dataset for: Effects of Corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus)



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R6.x804.000-0029-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Madeline Munoz-Bustamante
      Organisation name: 
          University of Miami / Rosenstiel School of Marine and Atmospheric Science
      Position name: 
          Program Manager
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  4600 Rickenbacker Cswy
              City: 
                  Miami
              Administrative area: 
                  Florida
              Postal code: 
                  33149
              Country: 
                  USA
              Electronic mail address: 
                  mbustamante@rsmas.miami.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-05-04T20:04:58+00:00
  Metadata standard name: 
      ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
  Metadata standard version: 
      ISO 19115-2:2009(E)
  Dataset URI: 
      https://data.gulfresearchinitiative.org/metadata/R6.x804.000:0029
Return To Index

Identification info: Data identification: Citation: Citation: Title: Dataset for: Effects of Corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus) Alternate title: Date: Date: Date: 2019-08-19 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/n7-sfa3-9041 title: DOI doi:10.7266/n7-sfa3-9041 Abstract: The goal of this project is to better understand the combined effects of oil and dispersant that larvae were likely exposed to after the spill. Mahi larvae will be exposed to varying sublethal concentrations of both Corexit alone and Corexit combined with slick oil. Transcriptional responses will be assessed using RNASeq after 48 hours of exposure. Thus this dataset consists of measurements of polycyclic aromatic hydrocarbons and dioctyl sodium sulfosuccinate (DOSS), videos of heart rate of mahi-mahi (Coryphaena hippurus) larva, phenotype images and larval RNA sequences. This dataset supports the publication: Greer, J. B., Pasparakis, C., Stieglitz, J. D., Benetti, D., Grosell, M., & Schlenk, D. (2019). Effects of corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus). Aquatic Toxicology, 212, 233–240. doi:10.1016/j.aquatox.2019.05.014 Purpose: To further understand the toxicity of Corexit and Corexit-oil mixtures on early life stage mahi-mahi. Status: Progress code: completed Point of contact: Responsible party: Individual name: Daniel Schlenk Organisation name: University of California Riverside / Department of Environmental Sciences Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 9518272018 Facsimile: Address: Address: Delivery point: 900 University Avenue Geology 2258 City: Riverside Administrative area: California Postal code: 92521 Country: USA Electronic mail address: daniel.schlenk@ucr.edu Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: mahi-mahi Keyword: cardiac development Keyword: transcriptomics Keyword: corexit Keyword: dispersant Keyword: chemical dispersion Keyword: Chemically-enhanced water-accommodated fractions (CEWAFs) Keyword: Coryphaena hippurus Keyword: Polyaromatic hydrocarbon Keyword: Developmental toxicity Keyword: Gene expression Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: inapplicable Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Greer, J.. 2019. Dataset for: Effects of Corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-sfa3-9041 Resource constraints: title: CC0 License Legal constraints: Use constraints: Restriction code: licenceUnrestricted Other constraints: This information is released under the Creative Commons license - No Rights Reserved - CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/). The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Resource constraints: title: Liability and Warranty Legal constraints: Other constraints: All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be submitted by an individual who represents and warrants that s/he has sufficient rights to be able to make the content available under a CC0 waiver. There is no warranty (expressed or implied) to these materials, their title, accuracy, non-infringement of third party rights, or fitness for any particular purpose, including the performance or results you may obtain from their use. Use these materials at your own risk. Under no circumstances shall GRIIDC be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use or the inability to use either this website or the materials available via this website. If you are dissatisfied with any website feature, content, or terms of use, your sole and exclusive remedy is to discontinue use. Aggregation Info: AggregateInformation: Aggregate Data Set Name: title: Related Publication Citation Citation: Title: Greer, J. B., Pasparakis, C., Stieglitz, J. D., Benetti, D., Grosell, M., & Schlenk, D. (2019). Effects of corexit 9500A and Corexit-crude oil mixtures on transcriptomic pathways and developmental toxicity in early life stage mahi-mahi (Coryphaena hippurus). Aquatic Toxicology, 212, 233–240. doi:10.1016/j.aquatox.2019.05.014 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1016/j.aquatox.2019.05.014 title: DOI doi:10.1016/j.aquatox.2019.05.014 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: biota Extent: Extent: Description: Dataset contains laboratory measurements of transcriptomic responses, no field sampling involved. Supplemental Information:
          Data is organized by different data types obtained from CEWAF and Corexit exposures.  Below are short descriptions of the data in each file and folder.   Folder: Water Chemistry Data = Raw data of PAH and DOSS concentrations. Contains the files titled "Phenotype_initial_PAH_DOSS", "Phenotype_final_PAH", "Phenotype_PAH_geometric", and "RNASeq_PAH_DOSS".  -Phenotype_initial_PAH_DOSS - Raw values of measured PAH and DOSS concentrations in micrograms per liter (µg/L) in water samples taken at the beginning of phenotype studies in December, 2018.   -Phenotype_final_PAH - Raw values of measured PAH concentrations in micrograms per liter (µg/L) in water samples taken at the end of the phenotype studies.  -RNASeq_PAH_DOSS - Raw values of measured PAH and DOSS concentrations in micrograms per liter (µg/L) in water samples taken at the beginning of the RNASeq study.  -Phenotype_PAH_geometric - summary of sumPAH concentrations in micrograms per liter (µg/L) for each CEWAF exposure in the phenotype study. sumPAH values represent the sum of 50 PAH analytes selected by the EPA based on individual toxicity and concentration. These values are calculated from the raw analytic data presented in the documents titled "Phenotype_initial_PAH" and "Phenotype_final_PAH" and are expressed here as the geometric mean of the sumPAH values from a sample taken at the beginning of the exposure, and sample taken at the end of exposure. --Exposure = Describes the nominal concentration of Corexit in milligrams per liter (mg/L) added to CEWAF preparation --sumPAH Initial (µg/L) = sumPAH values in micrograms per liter (µg/L) measured prior each exposure.  --sumPAH Final (µg/L) = sumPAH values in micrograms per liter (µg/L) measured at the conclusion of each exposure --sumPAH Geometric mean (µg/L) = geometric mean of initial and final PAH values in micrograms per liter (µg/L)  Phenotypic_measurements = Heart rate, pericardial area, yolk sac area, and eye diameter measurements after exposure --Treatment = Describes the treatment for each exposure group. Embryos were exposed to either seawater control, Corexit 9500A or CEWAF. Corexit 9500A concentrations are reported as DOSS concentration in micrograms per liter, measured prior to exposure and reported in the document titled "Phenotype_initial_PAH_DOSS". CEWAF exposures are reported as the sumPAH in micrograms per liter + DOSS concentration in micrograms per liter. sumPAH values represent the sum of 50 PAH analytes selected by the EPA based on individual toxicity and concentration. These values are calculated from the raw analytical data presented in the document titled "Phenotype_initial_PAH_DOSS" and "Phenotype_final_PAH_DOSS" and are presented as the geometric mean of the sumPAH values from initial and final PAH samples. The calculations for geometric mean are presented in "Phenotype_PAH_geometric". Measured DOSS concentration from CEWAF preparations are reported in the document titled "Phenotype_initial_PAH_DOSS". --Replicate = Biological replicate number within each exposure group --Number of heart beats (15 s) = Number of heart beats counted in 15 second video clips. Individual videos can be found in the folder titled "Heart_rate_videos". --Heart rate (beats per min) = Heart rate per minute, calculated by multiplying the number of heart beats in 15 sec * 4.  --Pericardial Area (pixels) = measured pericardial area in pixels from images contained in the folder "Phenotype_images". --Yolk Sac Area (pixels) = measured yolk sac are in pixels from images contained in the folder "Phenotype_images". --Eye diameter (length in pixels) = measured eye diameter in pixels from images contained in the folder "Phenotype_images". Eye diameter was unable to be calculated in some images due to low resolution of eye perimeter, in which case a "." has been added to the field  Folder: Phenotype_images - contains images taken at 4x zoom for measurements of pericardial area, eye diameter, and yolk sac area. Images are labeled as Treatment_concentration_replicate, where low, medium, and high concentrations represent increasing Corexit concentrations. For example, Corexit_low_1 represents the lowest Corexit concentration (2.5 mg/L nominal), replicate 1. CEWAF_med_3 represents CEWAF exposure at the medium Corexit concentration (5 mg/L nominal), replicate 3.  Folder: Heart_rate_videos - contains 15-20 second video clips at 8x zoom for measurements of heart rate. Videos are labeled similarly to "Phenotype_images" and are from the same replicates as phenotype images.
          
Dataset also contains the accession number/sample ID datasheet (SRA_accessions_S202.xlsx).|Chemically-enhanced water-accommodated fractions (CEWAFs) were prepared from oil samples collected at the surface during the DWH oil spill. CEWAFs were prepared with 1 g of oil per 1 L of filtered seawater with varying concentrations of Corexit 9500A added (final nominal concentrations: 2.5, 5, or 10 mg/L Corexit). The mixtures were stirred overnight in the dark with a minimal vortex, then allowed to settle for 3-6 hours prior to use. The lower 90% of the mixture was then drained and retained for subsequent use as 100% CEWAF (unfiltered) that was diluted to 5% using UV-sterilized seawater for test exposures. Corexit 9500A only exposures were prepared in a similar manner, without the addition of oil, and diluted to the same final nominal concentrations Corexit concentrations as CEWAFs. Mahi embryos (~8 hpf) were exposed to control seawater, CEWAFs, or Corexit 9500A preparations described above for 48 h. Four replicates were performed for each exposure for RNASeq, and 8 replicates were performed for phenotypes, with each replicate containing 30 embryos. Exposures were performed twice, once for phenotypic analysis, and once for RNA sequencing collection, each described below. During each experiment temperature, pH, dissolved oxygen, and salinity were monitored daily. Total ammonia was measured at the end of the exposure for the phenotype experiment, but was not performed in the RNAseq experiment. Water chemistry analysis for total PAHs and DOSS concentration were also performed in each experiment. For the phenotypic study samples were taken prior to exposure and at the end of the testing period. For the RNASeq study, PAH and DOSS measurements were only collected prior to exposure. Oil samples were collected in 250 mL amber glass bottles with no head space and immediately stored at 4 °C. Samples were analyzed by ALS Environmental using GC/MS-SIM. Mortality was assessed from each treatment prior to downstream phenotypic assessment or RNA sequencing. For phenotypic analysis, 10 randomly chosen larvae were collected from each treatment, place in 2% methylcellulose in seawater, and imaged on a Nikon SMZ800 stereomicroscope. Images were assessed for pericardial area, yolk sac area, and eye diameter using ImageJ version 1.52a. Heart rate was determined by counting the number of heart beats in 15 second video clips. For RNASeq, surviving embryos were collected from three beakers in each treatment and immediately frozen in liquid nitrogen. Larvae were homogenized, and total RNA extracted using the Qiagen RNeasy mini kit following the manufacturers recommendations. RNA concentration and quality were quantified using a Qubit Fluorometers and Agilent 2100 Bioanalyzer. Library preparations were then performed using the NEBNext Ultra II Directional RNA Library Prep Kit with 500 ng of total RNA as the starting input. Final libraries were multiplexed and sequenced on one lane of an Illumina NextSeq500 high-throughput sequencer and raw reads were submitted to the NCBI SRA database (Accession: PRJNA512294). Adapter sequences were trimmed from the raw reads using trimmomatic (v0.36), followed by quality control with FastQC (v0.11.7). Trimmed reads were pooled and used to assemble a de novo transcriptome with Trinity (version 2.6.6). Transcript quantification for each sample was performed using RSEM (v1.3.0) and differential expression analysis with DESeq2 (v1.20.0) with differential expression defined as p £ 0.05 after Benjamini-Hochberg false discovery rate correction.||||
Return To Index

Distribution info: Distribution: Distributor: Distributor: Distributor contact: Responsible party: Organisation name: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) Contact info: Contact: Phone: Telephone: Voice: 3618253604 Address: Address: Delivery point: 6300 Ocean Drive City: Corpus Christi Administrative area: TX Postal code: 78412 Country: USA Electronic mail address: griidc@gomri.org Online Resource: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org Role: Role code: distributor Distributor format: Format: Name: mov, jpg, xls, xlsx, txt, fasta Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 521.2423 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R6.x804.000:0029 Protocol: https Name: Data Landing Page Description: GRIIDC dataset landing page Function: Online function code: information
Return To Index

Metadata maintenance: Maintenance information: Maintenance and update frequency: unknown Maintenance note: This ISO metadata record was automatically generated from information provided to GRIIDC for dataset: R6.x804.000:0029 on 2021-07-29T05:04:14-05:00
Return To Index

Dataset Links: