Metadata: 
  File identifier: 
      R4.x263.189-0010-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Kathleen (Kathy) Schwehr
      Organisation name: 
          Texas A&M University at Galveston / Marine Sciences Department
      Position name: 
          Associate Research Scientist
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  4097404452
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  P.O. Box 1675
              City: 
                  Galveston
              Administrative area: 
                  Texas
              Postal code: 
                  77553
              Country: 
                  USA
              Electronic mail address: 
                  schwehrk@tamug.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2019-02-22T21:18:49+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.x263.189:0010
Return To Index
  Identification info: 
    Data identification: 
      Citation: 
        Citation: 
          Title: 
              Eukaryotic community response to oil and Corexit in a coastal water mesocosm, August 2015
          Alternate title: 
              Illumina HiSeq (100 bp PE) raw reads from coastal mesocosm study
          Date: 
            Date: 
              Date: 
                  2019-02-22
              Date type: 
                Date type code: 
                  publication
          Identifier: 
            Identifier: 
              Code: 
                Anchor: xlink: https://dx.doi.org/10.7266/n7-kvpb-0878 title: DOI
                  doi:10.7266/n7-kvpb-0878
      Abstract: 
          Illumina HiSeq (100 bp PE) mRNA sequence from a eukaryotic fraction of the microbial community. Samples were 
          collected from coastal mesocosm studies to assess the response of the planktonic community to exposure to 
          oil and Corexit. The content of this dataset includes the location in NCBI of 6 RNA sequencing samples for 
          eukaryotic plankton for the ADDOMEx mesocosm experiment, a Test of Coastal water with coastal microbial 
          concentrate, TeCOAST (Mesocosm 1). This dataset also includes the SraRunTable (biosample accession 
          SAMN05615432 at https://www.ncbi.nlm.nih.gov/biosample/5615432) for these data.
      Purpose: 
          RNA was extracted from samples at the end of the mesocosm experiment to enable analysis of eukaryotic 
          community structure and relative transcript abundance in response to oil (WAF; water accommodated fraction) 
          and Corexit enhanced WAF (CEWAF and dilute CEWAF; chemically enhanced water accommodated fraction) treatments.
      Status: 
        Progress code: 
          completed
      Point of contact: 
        Responsible party: 
          Individual name: 
              Zoe Finkel
          Organisation name: 
              Mount Allison University / Department of Geography and Environment
          Position name: 
              Professor
          Contact info: 
            Contact: 
              Phone: 
                Telephone: 
                  Voice: 
                      5063642615
                  Facsimile: 
              Address: 
                Address: 
                  Delivery point: 
                      144 Main St.
                  City: 
                      Sackville
                  Administrative area: 
                      New Brunswick
                  Postal code: 
                      E4L 1A8
                  Country: 
                      CAN
                  Electronic mail address: 
                      zfinkel@mta.ca
          Role: 
            Role code: 
              pointOfContact
      Point of contact: 
        Responsible party: 
          Individual name: 
              Andrew Irwin
          Organisation name: 
              Mount Allison University / Mathematics and Computer Science
          Position name: 
              Associate Professor
          Contact info: 
            Contact: 
              Phone: 
                Telephone: 
                  Voice: 
                      5063645747
                  Facsimile: 
              Address: 
                Address: 
                  Delivery point: 
                      62 York St.
                  City: 
                      Sackville
                  Administrative area: 
                      New Brunswick
                  Postal code: 
                      E4L 1E2
                  Country: 
                      CAN
                  Electronic mail address: 
                      airwin@mta.ca
          Role: 
            Role code: 
              pointOfContact
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              Illumina HiSeq (100 bp PE) mRNA sequence
          Keyword: 
              Eukaryotic community response
          Keyword: 
              oil
          Keyword: 
              WAF
          Keyword: 
              CEWAF
          Keyword: 
              Corexit
          Keyword: 
              phytoplankton response
          Type: 
            Keyword type code: 
              theme
      Descriptive keywords: 
        Keywords: 
          Keyword: 
            inapplicable
          Type: 
            Keyword type code: 
              place
      Resource constraints:  title: Cite As
        Constraints: 
          Use limitation: 
              Zoe Finkel, Andrew Irwin. 2019. Eukaryotic community response to oil and Corexit in a coastal water 
              mesocosm, August 2015. 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-kvpb-0878
      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.
      Language: 
          eng; USA
      Topic category: 
        Topic category code: 
          oceans
      Topic category: 
        Topic category code: 
          biota
      Topic category: 
        Topic category code: 
          environment
      Extent: 
        Extent: 
          Description: 
              Dataset contains Illumina HiSeq (100 bp PE) mRNA sequence from eukaryotes in coastal water mesocosm, no 
              field sampling involved.
      Supplemental Information: 
          Raw reads from Illumina HiSeq
          
          MESO1=mesocosm 1, TeCOAST;
          WC=water column;
          Bot=bottom, the accumulated marine snow in the bottom of one replicate from each treatment;
          1, 2, 3 or 2, 3, 4= replicate number;
          Treatments of control, WAF, CEWAF, and dilute CEWAF (DCEWAF) are described in the methods section. Briefly, 
          control is Gulf of Mexico seawater with no additions, WAF is water accommodated fraction, CEWAF is 
          chemically enhanced WAF (Corexit + WAF), and DCEWAF is diluted CEWAF. Concentrations are given in the methods.
          
          All samples were taken at the end of the experiment (74 hours). Samples can be found at NCBI under accession 
          numbers:
          MESO1-WC1: water column, control: SRR4238820
          MESO1-WC2: water column, WAF: SRR4238822
          MESO1-WC3: water column, CEWAF: SRR4238824
          MESO1-Bot2: bottom sample, WAF: SRR4238825
          MESO1-Bot3: bottom sample, CEWAF: SRR4238826
          MESO1-Bot4: bottom sample, dilute CEWAF: SRR4238833|TeCOAST (Mesocosm 1): mesocosms for a Test of Coastal 
          water with coastal microbial concentrate
          The seawater used in the TeCOAST mesocosm studies was collected on July 30, 2015, from 8 kilometers offshore 
          south of Galveston (TX) in the Gulf of Mexico. The salinity was 34. The seawater was processed through a 
          charcoal filter to remove large particles and debris. Four mesocosm tanks were treated in the following way. 
          The control tank was filled with the seawater directly from the storage tank of filtered seawater. This 
          seawater was also used to fill 130 L recirculating glass flumes to make water accommodated fraction (WAF) 
          and a chemically enhanced water accommodated fraction of oil (CEWAF). The WAF was prepared by mixing a total 
          of 24 mL (2 ml to start, 2 ml after 1 hr, then 5 ml at ~ 2, 3, 4 and 5 hrs total of 24 ml) of Macondo 
          surrogate Marlin oil into 130 L of the seawater. Total mixing time from the start of oil addition to 
          transfer to the mesocosms was 18 hrs. The WAF (79 L) was transferred to the WAF mesocosm tank and mixed. In 
          order to make CEWAF, Corexit 9500 was mixed with Macondo Surrogate oil in a ratio of 1:20 (Corexit to oil) 
          and 24 mL of this mixture (2 ml to start, 2 ml after 1 hr, then 5 ml at ~ 2, 3, 4 and 5 hrs total of 24 ml) 
          of surrogate oil plus Corexit was added to 130 L of seawater and mixed for 18 hrs. The CEWAF (79 L) was 
          transferred to the WAF mesocosm tank and mixed. In addition a dilute CEWAF (DCEWAF) mesocosm treatment was 
          produced by adding 9 L of CEWAF to 70 L of the original seawater for a total volume of 79 L. Light dark 
          bottles were also filled from the WAF and CEWAF. Plankton (≥63 µm) samples were collected using a net and 
          transferred into polycarbonate bottles. This concentrated plankton mass was introduced to each mesocosm and 
          stirred (2 L to each tank for a final volume 81 L) immediately prior to starting the experiments. No 
          plankton was added to the light or dark bottles. The EOE concentration for the control, WAF, DCEWAF and 
          CEWAF at the start of the experiments were estimated as 0 mg/L, 3.4 mg/L, 3.6 mg/L and 36 mg/L, 
          respectively. The EOE concentration of the control, WAF, DCEWAF and CEWAF mesocosms averaged for samples 
          taken during the first 74 hours were 0 mg/L , 1.21 mg/L, 4.28 and 43.4 mg/L, respectively. All mesocosms had 
          loses of EOE from 88 to 100%, while the bottles had losses of 56 to 74%.
          
          Estimated Oil Equivalence (EOE)
          The estimated oil equivalents (EOE) were determined by fluorescence (Wade et al. 2011) using Macondo surrogate 
          oil as a standard to produce calibration curves at 5 to 7 concentrations. Water samples (5 to 20 ml) were 
          extracted with 5 ml of dichloromethane. An aliquot of the extract was placed in a cuvette for fluorescence 
          analyses (Horiba Scientific Aqualog Fluorometer). The EOE were determined from the calibration curve (Wade 
          et al. 2011). Samples with fluorescence responses that exceeded the calibration curve were diluted so that 
          their fluorescence was within the calibration range. Samples were taken at the beginning and end of the 
          experiment and at intervals in between and at the same time point as measurements of other parameters during 
          the experiment.
          
          Eukaryotic metatranscriptome sampling and analysis
          Samples were taken for RNA extraction and sequencing at time t = 74 h from the mesocosm water column for 3 
          treatments (control, WAF, CEWAF) and from the bottom sediment of 3 treatments (WAF, CEWAF, DCEWAF). Filters 
          were immediately frozen at –80°C. RNA extraction was performed using standard protocols. Sequencing was 
          performed on an Illumina HiSeq 2000 at the McGill University Genome Quebec Innovation Centre 
          (http://gqinnovationcenter.com/index.aspx) using the TruSeq mRNA stranded mRNA protocols. Raw reads from the 
          sequencing pipeline were deposited in the NCBI SRA.||Two samples were taken from each mesocosm (control, 
          WAF, CEWAF, dilute CEWAF) at the end of the experiment, one in the water column and one from the bottom 
          layer with accumulated detritus.||Wade, T. L., Sweet, S. T., Walpert, J. N., Sericano, J. L., Singer, J. J., 
          & Guinasso, N. L. (2011). Evaluation of Possible Inputs of Oil From the Deepwater Horizon Spill to the Loop 
          Current and Associated Eddies in the Gulf of Mexico. Geophysical Monograph Series, 83–90. 
          doi:10.1029/2011gm001095
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: 
                  txt
              Version: 
                inapplicable
              File decompression technique: 
                  zip
          Distributor transfer options: 
            Digital transfer options: 
              Transfer size: 
                  0.0016
              Online: 
                Online Resource: 
                  Linkage: 
                    URL: 
                      https://data.gulfresearchinitiative.org/data/R4.x263.189:0010
                  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: 
          R4.x263.189:0010 on 2020-09-24T10:15:56-05:00
Return To Index