Metadata: 
  File identifier: 
      R4.x263.189-0011-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: 
      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.x263.189:0011
Return To Index
  Identification info: 
    Data identification: 
      Citation: 
        Citation: 
          Title: 
              Eukaryotic community response to oil and Corexit in a mesocosm, October 2015
          Alternate title: 
              Illumina HiSeq (100 bp PE) raw reads from coastal mesocosm study
          Date: 
            Date: 
              Date: 
                  2019-02-25
              Date type: 
                Date type code: 
                  publication
          Identifier: 
            Identifier: 
              Code: 
                Anchor: xlink: https://dx.doi.org/10.7266/n7-43q9-xq06 title: DOI
                  doi:10.7266/n7-43q9-xq06
      Abstract: 
          Samples were collected from coastal mesocosm studies to assess the response of the planktonic community to 
          exposure to oil and Corexit. This dataset includes the location of 12 RNA sequencing samples for eukaryotic 
          plankton for the ADDOMEx mesocosm experiment, Coastal water with coastal microbial concentrate, COAST 
          (mesocosm 2). This dataset also includes the SraRunTable (biosample accession SAMN09981213) at 
          https://www.ncbi.nlm.nih.gov/biosample/9981213 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: 
              Eukaryotic metatranscriptomes
          Keyword: 
              Illumina HiSeq
          Keyword: 
              Eukaryotic RNA
          Keyword: 
              WAF
          Keyword: 
              CEWAF
          Keyword: 
              DCEWAF
          Keyword: 
              oil
          Keyword: 
              Corexit
          Keyword: 
              mesocosm
          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 mesocosm, October 
              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/n7-43q9-xq06
      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 eukaryotic metatranscriptome analysis for plankton response to oil and Corexit, no field 
              sampling involved.
      Supplemental Information: 
          Raw reads from Illumina HiSeq.
          
          Samples can be found at NCBI under following library name and accession numbers:
          MESO2-CTRL_REP1: SRR7796775
          MESO2-CTRL_REP2: SRR7796776
          MESO2-CTRL_REP3: SRR7796777
          
          MESO2-WAF_REP1: SRR7796778
          MESO2-WAF_REP2: SRR7796784
          MESO2-WAF_REP3: SRR7796783
          
          MESO2-CEWAF_REP1: SRR7796781
          MESO2-CEWAF_REP2: SRR7796782
          MESO2-CEWAF_REP3: SRR7796773
          
          MESO2-DCEWAF_REP1: SRR7796774
          MESO2-DCEWAF_REP1: SRR7796779
          MESO2-DCEWAF_REP1: SRR7796780
          
          For library name: MESO2 = mesocosm 2, COAST; REP1, REP2, REP3 = replicate number; CTRL = Treatments of 
          control; WAF is water accommodated fraction; CEWAF is chemically enhanced WAF (Corexit + WAF) and DCEWAF is 
          diluted CEWAF.|Method for COAST, a mesocosm study using Gulf of Mexico coastal waters
          The seawater was collected from the same location as that used in TeCOAST mesocosm but was collected on 
          October 17 2015, from 8 kilometers offshore south of Galveston, Texas in the Gulf of Mexico. The salinity 
          was 31. The seawater was processed through a charcoal filter to remove large particles and debris. Four 
          treatments were prepared in triplicate. Control tanks were filled with seawater and a plankton mixture. 
          Water accommodated fraction (WAF) of oil was prepared by mixing 25 mL (5 ml ~ every 30 min for 2.5 hrs) of 
          Macondo surrogate oil into 130 L of seawater then mixing for 12 to 24 hrs. The WAF was then introduced into 
          the WAF mesocosm tanks and filled to 87 L and mixed. From these WAF tanks, 6 L was removed for other 
          experiments and analyses (2L for roller tables, 2 L dark/light, 4 L hydrocarbon analyses). In order to make 
          chemically enhanced water accommodated fraction (CEWAF), Corexit was mixed with oil in a ratio of 1:20 and 
          25 mL of this mixture (5 ml every 30 min for 2.5 hrs) of surrogate oil plus Corexit was added to 130 L of 
          seawater which was mixed for 8 to 24 hrs prior to being transferred to the mesocosm tanks. The CEWAF was 
          then introduced into the CEWAF mesocosm tanks and filled to 96 L and mixed. From these CEWAF tanks, 15 L was 
          removed for other experiments and analyses (9 L for the DCEWAF mesocosms, 2L for roller tables, 2 L 
          dark/light, 4 L hydrocarbon analyses). Diluted CEWAF (DCEWAF) was prepared by mixing 9 L of CEWAF with 78 L 
          of the original seawater for a total volume of 87 L. From these DCEWAF tanks 6 L was removed for other 
          experiments and analyses (2L for roller tables, 2 L dark/light, 4 L hydrocarbon analyses). Plankton (≥63 µm) 
          were collected using a net and transferred into polycarbonate bottles. This concentrated plankton mass was 
          introduced to the tanks and stirred (2 L to each final volume 83 L) immediately prior to starting the 
          experiments. The EOE mean concentration of the three mesocosms for the control, WAF, DCEWAF and CEWAF at the 
          start of the experiments were 0 mg/L, 0.26 mg/L, 2.74 mg/L and 41.5 mg/L, respectively. The EOE mean 
          concentration of the three for the control, WAF, DCEWAF and CEWAF mesocosms after 72 hours were 0 mg/L, 0.06 
          mg/L, 1.03, and 17.3 mg/L, respectively.
          
          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 = 72 h from each replicate and treatment (3 
          replicates x 4 treatments = 12 samples). 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, 
          https://www.ncbi.nlm.nih.gov/biosample/9981213.||||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: 
                  0.0019
              Online: 
                Online Resource: 
                  Linkage: 
                    URL: 
                      https://data.gulfresearchinitiative.org/data/R4.x263.189:0011
                  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.x263.189:0011 on 2021-08-02T21:25:56-05:00
Return To Index