MicroRNA sequencing data from Mahi exposed samples

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

DOI:
10.7266/N70Z71QJ
 
UDI:
R4.x258.000:0040
Last Update:
Sep 06 2017 15:53 UTC
 
Dataset Author(s):
Schlenk, Daniel; Diamante, Graciel
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-IV
 
Extent Description:
Dataset contains micro RNA sequencing, no field sampling involved.

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Schlenk, Daniel; Diamante, Graciel (2017) MicroRNA sequencing data from Mahi exposed samples. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University-Corpus Christi. doi:10.7266/N70Z71QJ

Abstract:

MicroRNAs (miRNA) play key roles in diverse biological processes including heart development. In our study, we evaluated the effects of DHW oil on miRNA expression in mahi-mahi (Coryphaena hippurus) embryos exposed to WAF from weathered slick oil and non-weathered source oil. miRNA and mRNA was compared using downstream bioinformatics with subsequent target organ predictions based on their interactions. Using two methods miRNA sequences were annotated using the Fugu rubripes genome or using BLAST. Our data showed that exposure of embryos to slick oil resulted in more differentially expressed (DE) miRNAs than source oil at all developmental stages 24hpf, 48hpf and 96hpf. There was also an increase in the number of DE miRNA as development progressed, 96h having the highest number of DE miRNAs. Gene ontology (GO) analysis on the target mRNAs was consistent with pathways analysis of miRNAs, predicting disruption of cardiovascular system development after oil exposure and showed specific miRNA–mRNA interactions that may contribute to these effects. This work is the first study linking miRNAs and mRNAs in fish responsive to DWH oil exposure, providing a new opportunity for better understanding of the molecular mechanism of DWH oil toxicity.

Purpose:

To further understand the role of microRNAs on oil induced toxicity at different time points during development.

Theme Keywords:

mahi mahi, microRNA, Slick Oil, Source Oil, Coryphaena hippurus

File Format:

xlsx

Filename:

GEO accession number.xlsx (53.14 KB)

Dataset Downloads:

5

MicroRNA sequencing data from Mahi exposed samples



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x258.000-0040-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: 
      2018-08-11T13:43:09+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.x258.000:0040
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Identification info: Data identification: Citation: Citation: Title: MicroRNA sequencing data from Mahi exposed samples Alternate title: Date: Date: Date: 2017-09-06 Date type: Date type code: creation Abstract: MicroRNAs (miRNA) play key roles in diverse biological processes including heart development. In our study, we evaluated the effects of DHW oil on miRNA expression in mahi-mahi (Coryphaena hippurus) embryos exposed to WAF from weathered slick oil and non-weathered source oil. miRNA and mRNA was compared using downstream bioinformatics with subsequent target organ predictions based on their interactions. Using two methods miRNA sequences were annotated using the Fugu rubripes genome or using BLAST. Our data showed that exposure of embryos to slick oil resulted in more differentially expressed (DE) miRNAs than source oil at all developmental stages 24hpf, 48hpf and 96hpf. There was also an increase in the number of DE miRNA as development progressed, 96h having the highest number of DE miRNAs. Gene ontology (GO) analysis on the target mRNAs was consistent with pathways analysis of miRNAs, predicting disruption of cardiovascular system development after oil exposure and showed specific miRNA–mRNA interactions that may contribute to these effects. This work is the first study linking miRNAs and mRNAs in fish responsive to DWH oil exposure, providing a new opportunity for better understanding of the molecular mechanism of DWH oil toxicity. Purpose: To further understand the role of microRNAs on oil induced toxicity at different time points during development. 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: microRNA Keyword: Slick Oil Keyword: Source Oil Keyword: Coryphaena hippurus Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: inapplicable Type: Keyword type code: place Language: eng; USA Topic category: Topic category code: biota Extent: Extent: Description: Dataset contains micro RNA sequencing, no field sampling involved. Supplemental Information: Number (NCBI GEO Accession number), File name, Stage (hpf), Concentration (g/L), Oil type (Control, Slick, or Source) microRNA expression analysis Data are available at NCBI Accession Number GSE102966, Bioproject Accession PRJNA399845 and SRA Study SRP116083|microRNA sequencing using NEBNext® Small RNA Library Prep Set for Illumina|NEXTseq v2|||
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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: xlsx Version: inapplicable File decompression technique: Distributor transfer options: Digital transfer options: Transfer size: 0.0531 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x258.000:0040 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.x258.000:0040 on 2019-11-13T22:33:27-06:00
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