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Annotated transcriptome and associated datasets of flatback mud crabs (Eurypanopeus depressus) exposed to dispersed oil

Deep-Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND)

DOI:
10.7266/N71C1TZC
 
UDI:
R4.x257.228:0013
Last Update:
Mar 24 2017 14:26 UTC
 
Dataset Author(s):
Vazquez-Miranda, Hernan; Thoma, Brent P; Wong, Juliet M; Felder, Darryl L; Crandall, Keith A, and Bracken-Grissom, Heather D
Point of Contact:
Vazquez Miranda, Hernan
Florida International University / Marine Sciences Program
Biscayne Bay Campus Marine Sciences Building, 3000 NE 151 St
North Miami, Florida  33181
USA
hvazquez@fiu.edu
Funding Source:
RFP-IV
Data Collection Period:
2014-09-23 to 2014-09-23

Identified Submitted Review Available
3 3 3 3

Abstract:

Flatback mud crab (Eurypanopeus depressus) transcriptome was assembled from 15 individuals sequenced in 2 Illumina HiSeq2000 lanes PE100 using Trinity2.0.3 and annotated with Trinotate2.0.1 on a custom MySQL database from The Broad Institute. We exposed 3 flatback mud crabs to one of 4 treatments (total = 12 individuals): non-aerated control, aerated control, oil only (Marlin platform Dorado 1g/l ), and oil-dispersant (Marlin platform Dorado 1g/l, COREXIT 9500 0.1g/l) for 72 hours to assess the up and down regulation of genes in muscle tissues. To account for stress caused by laboratory treatments, muscle tissue from three reference individuals that were sacrificed and not exposed to any lab treatments were analyzed. This dataset reports upregulated and downregulated gene expression. NCBI accession numbers are provided for each sample.

Purpose:

The objective of this study is to analyze the transcriptomic response via gene expression levels in mud crabs to dispersed oil using RNA-seq.

Theme Keywords:

RNA-seq, gene expression, gene ontology enrichment, oil spills, crabs, Eurypanopeus depressus

File Format:

csv, docx, fasta, xls, xlsx

Dataset Downloads:

0

Annotated transcriptome and associated datasets of flatback mud crabs (Eurypanopeus depressus) exposed to dispersed oil



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x257.228-0013-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Heather Bracken-Grissom
      Organisation name: 
          Florida International University / Marine Sciences Program
      Position name: 
          Assistant Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  3059194190
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  Biscayne Bay Campus
                  Marine Sciences Building, 3000 NE 151 St
              City: 
                  North Miami
              Administrative area: 
                  Florida
              Postal code: 
                  33181
              Country: 
                  USA
              Electronic mail address: 
                  heather.brackengrissom@fiu.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2018-08-11T13:28:47+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.x257.228:0013
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Identification info: Data identification: Citation: Citation: Title: Annotated transcriptome and associated datasets of flatback mud crabs (Eurypanopeus depressus) exposed to dispersed oil Alternate title: Mud crab transcriptome datasets Date: Date: Date: 2017-03-08 Date type: Date type code: creation Abstract: Flatback mud crab (Eurypanopeus depressus) transcriptome was assembled from 15 individuals sequenced in 2 Illumina HiSeq2000 lanes PE100 using Trinity2.0.3 and annotated with Trinotate2.0.1 on a custom MySQL database from The Broad Institute. We exposed 3 flatback mud crabs to one of 4 treatments (total = 12 individuals): non-aerated control, aerated control, oil only (Marlin platform Dorado 1g/l ), and oil-dispersant (Marlin platform Dorado 1g/l, COREXIT 9500 0.1g/l) for 72 hours to assess the up and down regulation of genes in muscle tissues. To account for stress caused by laboratory treatments, muscle tissue from three reference individuals that were sacrificed and not exposed to any lab treatments were analyzed. This dataset reports upregulated and downregulated gene expression. NCBI accession numbers are provided for each sample. Purpose: The objective of this study is to analyze the transcriptomic response via gene expression levels in mud crabs to dispersed oil using RNA-seq. Status: Progress code: completed Point of contact: Responsible party: Individual name: Hernan Vazquez Miranda Organisation name: Florida International University / Marine Sciences Program Position name: Postdoctoral Researcher Contact info: Contact: Phone: Telephone: Voice: Facsimile: Address: Address: Delivery point: Biscayne Bay Campus Marine Sciences Building, 3000 NE 151 St City: North Miami Administrative area: Florida Postal code: 33181 Country: USA Electronic mail address: hvazquez@fiu.edu Role: Role code: pointOfContact Point of contact: Responsible party: Individual name: Heather Bracken-Grissom Organisation name: Florida International University / Marine Sciences Program Position name: Assistant Professor Contact info: Contact: Phone: Telephone: Voice: 3059194190 Facsimile: Address: Address: Delivery point: Biscayne Bay Campus Marine Sciences Building, 3000 NE 151 St City: North Miami Administrative area: Florida Postal code: 33181 Country: USA Electronic mail address: heather.brackengrissom@fiu.edu Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: RNA-seq Keyword: gene expression Keyword: gene ontology enrichment Keyword: oil spills Keyword: crabs Keyword: Eurypanopeus depressus Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Gulf of Mexico Keyword: Texas Keyword: Florida Type: Keyword type code: place Language: eng; USA Topic category: Topic category code: biota Topic category: Topic category code: environment Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -80.33556 East bound longitude: -80.33556 South bound latitude: 27.43667 North bound latitude: 27.43667 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 27.43667 -80.33556 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2014-09-23 End date: 2014-09-23 Supplemental Information: Trinity gene number (gene_id), Trinity isoform number (transcript_id), SwissProt hit all ORFs (sprot_Top_BLASTX_hit), Uniprot90 hit all ORFs (TrEMBL_Top_BLASTX_hit), rRNA identity (RNAMMER), protein number (prot_id), protein coordinates, (prot_coords), SwissProt hit protein (sprot_Top_BLASTP_hit), UniProt90 hit protein (TrEMBL_Top_BLASTP_hit), Protein Family hit (Pfam), Signal Peptide hit (SignalP), Transmembrane HMMer hit (TmHMM), Gene Ontology eggnog (eggnog), Gene Ontology Blast (gene_ontology_blast), Gene Ontology Pfam (gene_ontology_pfam). |We conducted a de novo transcriptome assembly in TRINITY 2.0.3 using paired-end reads that passed QC from 15 total libraries. TRINITY was run on the FIU Panther Cluster in the High Performance Computer (HPC) environment with 24 cores and 256 GB of RAM with the following parameters: minimum kmer coverage of 4, maximum memory 252 GB, reverse single-stranded libraries, 24 CPUs, Butterfly maximum heap space 10GB, Butterfly initial heap space 10GB, Butterfly CPUs 24, and Inchworm CPUs 24. Trinotate was used to annotate the assembly. Gene expression and enrichment were calculated with edgeR, DESeq2, and GoSeq. Transcript and peptide columns were not used in this annotation. Raw data deposited directly to NCBI Genbank under: BioProject PRJNA376168 BioSamples SAMN06351232-SAMN06351246 TSA GFJG00000000 Eurypanopeus depressus Replicate 1. This Transcriptome Shotgun Assembly (TSA) project has been deposited at DDBJ/EMBL/GenBank under the accession GFJG00000000. The version described in this dataset is the first version, GFJG01000000. This submission includes one list of contents and 15 folders: DS1 – Complete transcriptomic assembly of 15 samples in Trinity fasta format, and spreadsheet with complete transcriptomic annotations for Eurypanopeus depressus from Trinotate. Columns include Trinity gene ID, transcript (isoform) ID, SwissProt Top BLASTX hit (sprot_Top_BLASTX), EMBL UniProt Top BLASTX Hit (TrEMBL_Top_BLASTX), RNAMMER hit, Protein Uniprot ID number (prot_id), protein coordinates (prot_coords), SwissProt Top BLASTP hit (sprot_Top_BLASTP), EMBL UniProt Top BLASTP Hit (TrEMBL_Top_BLASTP), Protein Family (Pfam), Signal Peptide (SignalP), Transmembrane HMMer (TmHMM), EggNog pathways, Gene Ontology (GO) from BLAST (gene_ontology_blast), and GO from Pfam (gene_ontology_pfam). DS2 – spreadsheet with significant regulated annotated genes from edgeR. Downregulated features in blue, and upregulated features in orange. DS3 – spreadsheet with significant regulated annotated isoforms from edgeR. Downregulated features in blue, and upregulated features in orange. DS4 – spreadsheet with significant regulated annotated genes from DESeq2. Downregulated features in blue, and upregulated features in orange. DS5 – spreadsheet with significant regulated annotated isoforms from DESeq2. Downregulated features in blue, and upregulated features in orange. DS6 – spreadsheet with counts of upregulated genes’ GOs from edgeR DS7 – spreadsheet with counts of upregulated isoforms’ GOs from edgeR DS8 – spreadsheet with counts of upregulated genes’ GOs from DESeq2 DS9 – spreadsheet with counts of upregulated isoforms’ GOs from DESeq2 DS10 – spreadsheet with counts of downregulated genes’ GOs from edgeR DS11 – spreadsheet with counts of downregulated isoforms’ GOs from edgeR DS12 – spreadsheet with counts of downregulated genes’ GOs from DESeq2 DS13 – spreadsheet with counts of downregulated isoforms’ GOs from DESeq2 DS14 – collection of spreadsheets with feature ranking by log2 fold change (logFC) from edgeR and DESeq2 feature counts between pairwise experimental condition comparisons (NC, OO, OD), P-values, and False Discovery Rate (FDR) adjustments, EMBL UniProt Top BLASTX Hit (TrEMBL_Top_BLASTX), and Gene Ontology (GO) from BLAST (gene_ontology_blast) DS15 - Gene Ontology term enrichment analyses with GOseq, based on gene count matrices from edgeR and DESeq2|Illumina HiSeq2000|||
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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: csv, docx, fasta, xls, xlsx Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 606.1289 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x257.228:0013 Protocol: https
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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.x257.228:0013 on 2018-12-18T10:51:24+00:00
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