Full View Normal View

data

De novo transcriptome of Mahi-mahi embryos

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

DOI:
10.7266/N7MW2F6S
 
UDI:
R4.x258.000:0002
Last Update:
Jun 30 2017 22:28 UTC
 
Dataset Author(s):
Xu, Elvis Genbo
Point of Contact:
Xu, Elvis Genbo
University of California Riverside / Department of Environmental Sciences
900 University Ave
Riverside, California  92521
USA
genboxu@126.com
Funding Source:
RFP-IV
 
Extent Description:
No field sampling was involved.

Identified Submitted Review Available
3 3 3 3

Abstract:

Total mRNA profiles of 24, 48, 96 hours post fertilization mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25, and resulted in a Trinity_fasta.txt file.

Purpose:

To provide molecular resources for facilitating further investigations on the holistic understanding of the developmental toxicity of DWH oil in mahi-mahi.

Theme Keywords:

Mahi-Mahi, mRNA Sequencing, De Novo Transcriptome, Embryo

File Format:

csv, txt, xls

Dataset Downloads:

0

De novo transcriptome of Mahi-mahi embryos



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x258.000-0002-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    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
  Date stamp: 
      2018-08-11T13:36:55+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.x258.000:0002
Return To Index

Identification info: Data identification: Citation: Citation: Title: De novo transcriptome of Mahi-mahi embryos Alternate title: Date: Date: Date: 2016-09-23 Date type: Date type code: publication Abstract: Total mRNA profiles of 24, 48, 96 hours post fertilization mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25, and resulted in a Trinity_fasta.txt file. Purpose: To provide molecular resources for facilitating further investigations on the holistic understanding of the developmental toxicity of DWH oil in mahi-mahi. Status: Progress code: completed Point of contact: Responsible party: Individual name: Elvis Genbo Xu Organisation name: University of California Riverside / Department of Environmental Sciences Position name: Postdoctoral Fellow Contact info: Contact: Phone: Telephone: Voice: 9513137643 Facsimile: Address: Address: Delivery point: 900 University Ave City: Riverside Administrative area: California Postal code: 92521 Country: USA Electronic mail address: genboxu@126.com Role: Role code: author 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: mRNA Sequencing Keyword: De Novo Transcriptome Keyword: Embryo 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: No field sampling was involved. Supplemental Information: trinity_fasta.txt: mRNA profiles pooled and assembled with Trinity (k-mer lenth set at 25) sample infor.csv: GEO accession number, sample number, status, note, species, age, concentration (ng/ul) Trinotate.xls: #gene_id, transcript_id, sprot_Top_BLASTX_hit, TrEMBL_Top_BLASTX_hit, RNAMMER, prot_id, prot_coords, sprot_Top_BLASTP_hit, TrEMBL_Top_BLASTP_hit, Pfam, SignalP, TmHMM, eggnog, gene_ontology_blast, gene_ontology_pfam, transcript, peptide |Total mRNA profiles of 24, 48, 96 hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. All reads were pooled and assembled de novo using Trinity (version 2.2.0) with k-mer length set at 25, and resulted a Trinity_fasta.txt file.|Illumina HiSeq2500, Biocluster|||GEO Accession Number: GSE79675
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: csv, txt, xls Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 23.0966 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x258.000:0002 Protocol: https
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.x258.000:0002 on 2018-08-19T01:39:22+00:00
Return To Index