Time Course Crude Oil Exposures of Early Life Stage Mahi-Mahi for RNA-Seq and Assessment of Cardiotoxicity

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

DOI:
10.7266/N7K35S21
 
UDI:
R4.x258.258:0005
Last Update:
Sep 22 2016 17:24 UTC
 
Dataset Author(s):
Edward Mager, Ph.D.
Point of Contact:
Munoz-Bustamante, Madeline
University of Miami / Rosenstiel School of Marine and Atmospheric Science
4600 Rickenbacker Cswy
Miami, Florida  33149
USA
mbustamante@rsmas.miami.edu
Funding Source:
RFP-IV
 
Extent Description:
All experiments were lab-based, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Edward Mager, Ph.D.. 2016. Time Course Crude Oil Exposures of Early Life Stage Mahi-Mahi for RNA-Seq and Assessment of Cardiotoxicity. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7K35S21

Abstract:

Three 96 h time course exposures were performed on freshly fertilized mahi-mahi embryos using two types of crude oil (slick (OFS) and source (Mass)) for the purposes of: (1) analyzing whole animal transcriptome responses by RNA-Seq/qPCR analysis, (2) phenotypic anchoring of transcriptional responses to cardiotoxic endpoints by imaging analysis of heart rate and pericardial and yolk sac edema and (3) obtaining additional replicates for qPCR to confirm transcriptional response of select genes identified by RNA-Seq. This dataset contains all of the data associated with the exposures and phenotypic analyses. This dataset also includes level thresholds (e.g., LC25, LC50) for two different weathered states of oil. Tests G001 and G002 were performed with slick (OFS) oil prepared as a high energy water-accommodated fraction (HEWAF). Test G001 failed to produce a dose response due to insufficient mortality; therefore, test G002 was performed as a repeat of test G001 using higher nominal HEWAF concentrations. Test G003 was performed with source (MASS) oil prepared as a HEWAF. Transcriptional response data (i.e. RNA-Seq and qPCR) are provided in a separate dataset (UDI: R4.x258.258:0001).

Purpose:

Phenotypic anchoring of transcriptional responses observed by RNA-Seq/qPCR to cardiotoxic endpoints by imaging analysis of heart rate and pericardial edema and establishing total PAH effect level thresholds for mortality of early life stage mahi-mahi.

Theme Keywords:

Cardiotoxicity, heart rate, pericardial edema, teleost, mahi-mahi, early life stage, crude oil, polycyclic aromatic hydrocarbons, gene expression, RNA-seq, phenotypic anchoring, Survival, Mortality, Bioassay, LC50

File Format:

csv, jpg, mp4

Filename:

R4 x258 258 0005 Time Course.zip (583.99 MB)

Dataset Downloads:

3

Time Course Crude Oil Exposures of Early Life Stage Mahi-Mahi for RNA-Seq and Assessment of Cardiotoxicity



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x258.258-0005-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Edward Mager
      Organisation name: 
          University of North Texas / Department of Biological Sciences
      Position name: 
          Assistant Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  940-369-8392
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  1155 Union Circle #310559
              City: 
                  Denton
              Administrative area: 
                  Texas
              Postal code: 
                  76203
              Country: 
                  USA
              Electronic mail address: 
                  Edward.Mager@unt.edu
          Online Resource: 
            Online Resource: 
              Linkage: 
                URL: 
                  http://biology.unt.edu/~mager/
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-05-04T20:04:56+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/R4.x258.258:0005
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Identification info: Data identification: Citation: Citation: Title: Time Course Crude Oil Exposures of Early Life Stage Mahi-Mahi for RNA-Seq and Assessment of Cardiotoxicity Alternate title: Phenotypic anchoring of cardiotoxic endpoints to transcriptional responses for mahi-mahi Date: Date: Date: 2016-09-23 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/N7K35S21 title: DOI doi:10.7266/N7K35S21 Abstract: Three 96 h time course exposures were performed on freshly fertilized mahi-mahi embryos using two types of crude oil (slick (OFS) and source (Mass)) for the purposes of: (1) analyzing whole animal transcriptome responses by RNA-Seq/qPCR analysis, (2) phenotypic anchoring of transcriptional responses to cardiotoxic endpoints by imaging analysis of heart rate and pericardial and yolk sac edema and (3) obtaining additional replicates for qPCR to confirm transcriptional response of select genes identified by RNA-Seq. This dataset contains all of the data associated with the exposures and phenotypic analyses. This dataset also includes level thresholds (e.g., LC25, LC50) for two different weathered states of oil. Tests G001 and G002 were performed with slick (OFS) oil prepared as a high energy water-accommodated fraction (HEWAF). Test G001 failed to produce a dose response due to insufficient mortality; therefore, test G002 was performed as a repeat of test G001 using higher nominal HEWAF concentrations. Test G003 was performed with source (MASS) oil prepared as a HEWAF. Transcriptional response data (i.e. RNA-Seq and qPCR) are provided in a separate dataset (UDI: R4.x258.258:0001). Purpose: Phenotypic anchoring of transcriptional responses observed by RNA-Seq/qPCR to cardiotoxic endpoints by imaging analysis of heart rate and pericardial edema and establishing total PAH effect level thresholds for mortality of early life stage mahi-mahi. Status: Progress code: completed Point of contact: 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 Point of contact: Responsible party: Individual name: Edward Mager Organisation name: University of North Texas / Department of Biological Sciences Position name: Assistant Professor Contact info: Contact: Phone: Telephone: Voice: 940-369-8392 Facsimile: Address: Address: Delivery point: 1155 Union Circle #310559 City: Denton Administrative area: Texas Postal code: 76203 Country: USA Electronic mail address: Edward.Mager@unt.edu Online Resource: Online Resource: Linkage: URL: http://biology.unt.edu/~mager/ Role: Role code: principalInvestigator Descriptive keywords: Keywords: Keyword: Cardiotoxicity Keyword: heart rate Keyword: pericardial edema Keyword: teleost Keyword: mahi-mahi Keyword: early life stage Keyword: crude oil Keyword: polycyclic aromatic hydrocarbons Keyword: gene expression Keyword: RNA-seq Keyword: phenotypic anchoring Keyword: Survival Keyword: Mortality Keyword: Bioassay Keyword: LC50 Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: inapplicable Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Edward Mager, Ph.D.. 2016. Time Course Crude Oil Exposures of Early Life Stage Mahi-Mahi for RNA-Seq and Assessment of Cardiotoxicity. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7K35S21 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: Xu, E. G., Mager, E. M., Grosell, M., Pasparakis, C., Schlenker, L. S., Stieglitz, J. D., … Schlenk, D. (2016). Time- and oil-dependent transcriptomic and physiological responses to Deepwater Horizon oil in mahi-mahi (Coryphaena hippurus) embryos and larvae. Environ. Sci. Technol. doi:10.1021/acs.est.6b02205 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1021/acs.est.6b02205 title: DOI doi:10.1021/acs.est.6b02205 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: biota Extent: Extent: Description: All experiments were lab-based, no field sampling involved. Supplemental Information: Heart rate (beats per minute), pericardial and yolk sac edema (pericardial area in pixels), survival, pH, dissolved oxygen (mg/L), salinity (ppt), ammonia (µM), PAH concentrations (µg/L), Date (DD-MM-YY), period (time period), water temperature (degree C), for video and image files the file name refers to the Tank ID Dilution or Stock Code and replicate (more information can be found in the Tank ID Dilution or Stock Code.csv files) Acute (96 h) Mahi-Mahi Early Life Stage Toxicity Testing: Experiment G001 using slick (OFS) oil prepared as a high energy water-accommodated fraction (HEWAF): Control treatment = 0% oil, Treatment 2 = 0.25% Slick oil, Treatment 3 = 0.5% Slick oil, Treatment 4 = 1% Slick oil, Treatment 5 = 2% Slick oil, Treatment 6 = 4% Slick oil. Experiment G002 using slick (OFS) oil prepared as a high energy water-accommodated fraction (HEWAF): Control treatment = 0% oil, Treatment 2 = 1% Slick oil, Treatment 3 = 2% Slick oil, Treatment 4 = 4% Slick oil, Treatment 5 = 8% Slick oil, Treatment 6 = 16% Slick oil. Experiment G003 using source (MASS) oil prepared as a high energy water-accommodated fraction (HEWAF): Control treatment = 0% oil, Treatment 2 = 0.125% Source oil, Treatment 3 = 0.25% Source oil, Treatment 4 = 0.5% Source oil, Treatment 5 = 1% Source oil, Treatment 6 = 2% Source oil. Four replicates per treatment: Control: C1-C4, Treatment 1: T1-T4, Treatment 2: T5-T8, Treatment 3: T9-T12, Treatment 4: T13-T16, Treatment 5: T17-T20. Ammonia: Standard curve, Rep (replicate), Avg (average), Regression, St Dev (Standard deviation), Conc (concentration). Fluorescence: Sample type, Sample ID, Nominal Dilution (%), Peak Area for Excitation Wavelength 1, Peak Area for Excitation Wavelength 2, Blank Subtracted Sum of Peak Areas 1 and 2, Log Nominal Dilution, Log Blank Subtracted Sum of Peak Areas 1 and 2, Dilution Factor, Measured Dilution (%). PAH Analysis: Units (ug/L), Component, Dilution Factor, Reporting Limit, Detection Limit, Result, Result Notes, Spike Concentration, Percent Recovery, Acceptance Limits, Average, RPD (relative percent difference), Retention Time, Regulatory Limit. Tank ID Dilution or Stock Code: Tank ID Dilution or Stock Code, Start Date, Start time, End date, End time, Nominal Treatment Concentration, Treatment Units, Replicate number. Test Performance Monitoring: Tank ID, Date, Time, Number at test start, Number observed treatment mortalities, Number from non-treatment mortality, Number observed alive. Water Quality Monitoring: Tank ID, Date, Time, Period (Initial, 24h, 48h, 72h, 96h), Water temp. (degrees C), pH, D.O. (mg/L), Salinity (ppt), Total ammonia (uM) |Heart rate was determined visually by counting heart beats from videos slowed to 0.5 speed. Pericardial area was measured using ImageJ version 1.46r from a perimeter drawn with the freehand tool enclosing this area |Nikon SMZ800 stereomicroscope with Fire-i400 or Fire-i530c camera, YSI ProODO oxygen meter, PHM201 pH meter, refractometer, Spectramax plate reader, GC/MS-SIM, LS45 fluorescence spectrometer|||
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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: csv, jpg, mp4 Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 583.994 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x258.258:0005 Protocol: https Name: Data Landing Page Description: GRIIDC dataset landing page Function: Online function code: information
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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: R4.x258.258:0005 on 2021-09-23T19:11:27-05:00
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