Transcriptome data from hepatopancreas and gill tissues of Callinectes sapidus (blue crabs) exposed to surrogate crude oil in the laboratory and laboratory controls

Continued Sampling of Blue Crab Larvae, Juveniles and Adults to Evaluate Oil Spill Effects on Population Connectivity and Adaptation, and Predict the Dynamics of Recovery

DOI:
10.7266/N70863Q3
 
UDI:
R3.x175.000:0002
Last Update:
Sep 14 2015 18:34 UTC
 
Dataset Author(s):
Yednock, Bree K. , Sullivan, Timothy J., and Joesph K. Neigel
Point of Contact:
Neigel, Joseph
University of Louisiana at Lafayette / Department of Biology
P.O.Box 42451
Lafayette, Louisiana  70504
USA
jneigel@louisiana.edu
Funding Source:
RFP-III
 
Extent Description:
Samples were collected at Cocodrie, LA (LUMCON, 29.254 and -90.6639) on 05/2011 for use in laboratory studies.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Yednock, Bree K. , Sullivan, Timothy J., and Joesph K. Neigel. 2015. Transcriptome data from hepatopancreas and gill tissues of Callinectes sapidus (blue crabs) exposed to surrogate crude oil in the laboratory and laboratory controls. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N70863Q3

Abstract:

In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. To characterize the blue crab transcriptome and identify genes that respond to oil exposure we sequenced transcriptomes from hepatopancreas and gill tissues of juvenile blue crabs exposed to a water-accommodated fraction of surrogate Macondo crude oil and compared those to transcriptomes from an unexposed control group. Illumina sequencing provided 42.5 million paired-end reads for the control group (3 individuals) and 44.9 million paired-end reads for the treatment group (4 individuals). These raw-reads are provided in the Bioproject 283615 deposited into NCBI (http://www.ncbi.nlm.nih.gov/bioproject/?term=283615). This dataset also includes data funded under RFP II R2.x214.000:0002.

Purpose:

This dataset was collected to evaluate the effects of oil spills on population connectivity and adaptation, and to predict the dynamics of population recovery.

Theme Keywords:

blue crab, Callinectes sapidus, transcriptome, population genetics

Dataset Downloads:

0

Transcriptome data from hepatopancreas and gill tissues of Callinectes sapidus (blue crabs) exposed to surrogate crude oil in the laboratory and laboratory controls



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R3.x175.000-0002-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Joseph Neigel
      Organisation name: 
          University of Louisiana at Lafayette / Department of Biology
      Position name: 
          Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  3374825661
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  P.O.Box 42451
              City: 
                  Lafayette
              Administrative area: 
                  Louisiana
              Postal code: 
                  70504
              Country: 
                  USA
              Electronic mail address: 
                  jneigel@louisiana.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-06-18T05:00:48+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/R3.x175.000:0002
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Identification info: Data identification: Citation: Citation: Title: Transcriptome data from hepatopancreas and gill tissues of Callinectes sapidus (blue crabs) exposed to surrogate crude oil in the laboratory and laboratory controls Alternate title: Callinectes sapidus (blue crabs) transcriptome. Date: Date: Date: 2015-09-14 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/N70863Q3 title: DOI doi:10.7266/N70863Q3 Abstract: In 2010 blue crabs in the northern Gulf of Mexico were exposed to crude oil and chemical dispersants from the Deepwater Horizon oil spill. To characterize the blue crab transcriptome and identify genes that respond to oil exposure we sequenced transcriptomes from hepatopancreas and gill tissues of juvenile blue crabs exposed to a water-accommodated fraction of surrogate Macondo crude oil and compared those to transcriptomes from an unexposed control group. Illumina sequencing provided 42.5 million paired-end reads for the control group (3 individuals) and 44.9 million paired-end reads for the treatment group (4 individuals). These raw-reads are provided in the Bioproject 283615 deposited into NCBI (http://www.ncbi.nlm.nih.gov/bioproject/?term=283615). This dataset also includes data funded under RFP II R2.x214.000:0002. Purpose: This dataset was collected to evaluate the effects of oil spills on population connectivity and adaptation, and to predict the dynamics of population recovery. Status: Progress code: completed Point of contact: Responsible party: Individual name: Joseph Neigel Organisation name: University of Louisiana at Lafayette / Department of Biology Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 3374825661 Facsimile: Address: Address: Delivery point: P.O.Box 42451 City: Lafayette Administrative area: Louisiana Postal code: 70504 Country: USA Electronic mail address: jneigel@louisiana.edu Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: blue crab Keyword: Callinectes sapidus Keyword: transcriptome Keyword: population genetics Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: inapplicable Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Yednock, Bree K. , Sullivan, Timothy J., and Joesph K. Neigel. 2015. Transcriptome data from hepatopancreas and gill tissues of Callinectes sapidus (blue crabs) exposed to surrogate crude oil in the laboratory and laboratory controls. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N70863Q3 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: Yednock, B. K., Sullivan, T. J., & Neigel, J. E. (2015). De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil. BMC Genomics, 16(1). doi:10.1186/s12864-015-1739-2 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1186/s12864-015-1739-2 title: DOI doi:10.1186/s12864-015-1739-2 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: biota Extent: Extent: Description: Samples were collected at Cocodrie, LA (LUMCON, 29.254 and -90.6639) on 05/2011 for use in laboratory studies. Supplemental Information: isolate type and raw transcriptomic sequence reads. The dataset contains 4 files 1 per sequence read archive (SRA): juvenile blue crab gill control,juvenile blue crab hepatopancreas control, juvenile blue crab gill tissue after oil treatment, juvenile blue crab hepatopancreas tissue after oil treatment.|Treatment blue crabs were exposed to crude oil at a concentration of 2.5 ppm for 24 hours||||
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Distribution info: Distribution: Distributor: Distributor: Distributor contact: Responsible party: Organisation name: NCBI Contact info: Contact: Phone: Telephone: Voice: 3014962475 Address: Address: Delivery point: National Library of Medicine 8600 Rockville Pike City: Bethesda Administrative area: Maryland Postal code: 20894 Country: USA Electronic mail address: info@ncbi.nlm.nih.gov Online Resource: Online Resource: Linkage: URL: https://www.ncbi.nlm.nih.gov Role: Role code: distributor Distributor format: Format: Name: Version: inapplicable File decompression technique: Distributor transfer options: Digital transfer options: Transfer size: Online: Online Resource: Linkage: URL: http://www.ncbi.nlm.nih.gov/bioproject/?term=283615 Protocol: http Name: missing Description: missing Function: missing
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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: R3.x175.000:0002 on 2021-06-18T10:38:51-05:00
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