Transcriptional alterations in mahi-mahi (Coryphaena hippurus) mucus following oil exposure

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

DOI:
10.7266/n7-m7d5-nk45
 
UDI:
R6.x804.000:0036
Last Update:
Jun 27 2019 18:32 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 transcriptional alterations, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Greer, J.. 2019. Transcriptional alterations in mahi-mahi (Coryphaena hippurus) mucus following oil exposure. 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-m7d5-nk45

Abstract:

The goal of this project is to perform RNASeq on mucus collected from juvenile mahi-mahi (Coryphaena hippurus) following oil exposure. ~30-day old mahi-mahi was exposed to 5 or 10% HEWAF (high energy water accommodated fraction) dilutions for 48 hours. Following exposure, mucus was collected and RNASeq was performed to identify differentially expressed transcripts. In addition, water quality measurements and levels of polycyclic aromatic hydrocarbons (PAHs) were made. These transcripts could provide target genes that could be used as biomarkers for non-invasive identification of oil exposure in fish.

Purpose:

To assess the use of mucosal RNA for biomarker identification in oil exposed mahi.

Theme Keywords:

mahi-mahi, coryphaena hippurus, epidermal mucus, transcriptomics, mucosal RNA, biomarker identification, High energy water accommodated fraction (HEWAF), Polycyclic aromatic hydrocarbons (PAH)

File Format:

xls, txt, xlsx, fasta

Filename:

R6x8040000036 Mahi Mucus.zip (52.96 MB)

Dataset Downloads:

2

Transcriptional alterations in mahi-mahi (Coryphaena hippurus) mucus following oil exposure



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R6.x804.000-0036-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.x804.000:0036
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Identification info: Data identification: Citation: Citation: Title: Transcriptional alterations in mahi-mahi (Coryphaena hippurus) mucus following oil exposure Alternate title: Date: Date: Date: 2019-08-09 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/n7-m7d5-nk45 title: DOI doi:10.7266/n7-m7d5-nk45 Abstract: The goal of this project is to perform RNASeq on mucus collected from juvenile mahi-mahi (Coryphaena hippurus) following oil exposure. ~30-day old mahi-mahi was exposed to 5 or 10% HEWAF (high energy water accommodated fraction) dilutions for 48 hours. Following exposure, mucus was collected and RNASeq was performed to identify differentially expressed transcripts. In addition, water quality measurements and levels of polycyclic aromatic hydrocarbons (PAHs) were made. These transcripts could provide target genes that could be used as biomarkers for non-invasive identification of oil exposure in fish. Purpose: To assess the use of mucosal RNA for biomarker identification in oil exposed 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: coryphaena hippurus Keyword: epidermal mucus Keyword: transcriptomics Keyword: mucosal RNA Keyword: biomarker identification Keyword: High energy water accommodated fraction (HEWAF) Keyword: Polycyclic aromatic hydrocarbons (PAH) 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. Transcriptional alterations in mahi-mahi (Coryphaena hippurus) mucus following oil exposure. 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-m7d5-nk45 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., Andrzejczyk, N. E., Mager, E. M., Stieglitz, J. D., Benetti, D., Grosell, M., & Schlenk, D. (2019). Whole-Transcriptome Sequencing of Epidermal Mucus as a Novel Method for Oil Exposure Assessment in Juvenile Mahi-Mahi (Coryphaena hippurus). Environmental Science & Technology Letters, 6(9), 538–544. doi:10.1021/acs.estlett.9b00479 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1021/acs.estlett.9b00479 title: DOI doi:10.1021/acs.estlett.9b00479 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: biota Extent: Extent: Description: Dataset contains laboratory measurements of transcriptional alterations, no field sampling involved. Supplemental Information: Data is organized by different data types obtained from HEWAF exposures of juvenile mahi. Below are short descriptions of the data in each file:
          
The file "Trinity.fasta" contains - Transcriptome assembly of raw reads using Trinity, after rRNA removal with sortMeRNA. The raw sequencing data can be found in the NCBI SRA database, Accession: PRJNA526742.
          
The file "S203 Fluorescence Analysis.xlsx" contains - PAH Fluorescence measurements: Raw fluorescence measurements used to calculate initial and final PAH concentrations from each day of the exposure. --Day = Day of sample collection. A water change was performed 24 hours after the start of exposure. Day 1 encompasses the first 24 hours prior to the water change, and day 2 encompasses the final 24 hours after the water change --Sample Type = Describes if the sample was from a standard PAH solution used to generate the standard curve, or if the sample was collected from WAFs prepared for exposures. --Sample Id = identification number used to uniquely identify the sample --Nominal Dilution (%) = For standard curve samples (identified under "sample type"), describes the dilution of the PAH standard for standard curve formation. Control sample was fresh seawater. WAF dilution series with a dilution of 0 was taken from the seawater control tanks during the experiment and was not diluted. 5% and 10% WAF dilutions are samples collected from the HEWAF dilutions used for exposure. --Peak Area for Excitation Wavelength 1 = Calculated area under the curve for wavelength 1, ~224 nm. --Peak Area for Excitation Wavelength 2 = Calculated area under the curve for wavelength 2, ~258 nm. --Blank Subtracted Sum of Peak Areas 1+2 = Calculated sum of the total area under the curve for wavelengths 1 and 2, minus the sum of the areas under the curve for the control sample --Log Nominal Dilution = Log value of the nominal dilution in the standard curve samples --Log Blank Subtracted Sum of Peak Areas 1+2 = Log of the value calculated in the "Blank Subtracted Sum of Peak Areas 1+2" column. --Dilution Factor = For WAF preparations, describes if the sample was diluted prior to analysis --Measured Dilution (%) = 10^((Log blank subtracted sum of peak areas 1+2 - y-intercept) / calculated slope) * Dilution factor --Notes = For WAF preparations, describes if the sample was an initial value immediately after WAF preparation or the final value prior to the water change (day 1) or immediately prior to the end of the experiment (day 2). --Standard curve parameters = category of parameters for the standard curve --Standard curve values = values determined for each standard curve parameter
          
The file "HEWAF stock concentrations.xls" contains - HEWAF stock concentrations and includes raw values of measured PAH concentrations in micrograms per liter (µg/L) in water samples taken from the 10% HEWAF exposure at the beginning of each day.
          
The file "SRA_accessions.xlsx" contains sample ID and accession numbers in the NCBI Sequence Read Archive (SRA) for the raw sequencing reads. Accession (SRA accession number for each biological sample, unique to each sample), Title (Title for each sample, and includes the HEWAF percentage, followed by the biological replicate number), BioProject (Accession number for the NCBI BioProject), BioSample (Unique accession number for each biological sample in the SRA database), and SRA.filename (Filename in the SRA data for the raw sequencing data associated with each BioSample).
          
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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: xls, txt, xlsx, fasta Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 52.9646 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R6.x804.000:0036 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: R6.x804.000:0036 on 2021-07-29T04:40:33-05:00
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