1. Home
  2. Data Publication
Correlating gene expression profiles with CO2 treatment and OA-affected behaviours in the two-toned pygmy squid (Idiosepius pygmaeus)
We correlated transcriptomic data from the central nervous system (CNS) and eyes of male two-toned pygmy squid (Idiosepius pygmaeus) with CO2 treatment levels and OA-affected behaviours in the same individuals to identify genes potentially contributing to OA-induced behavioural changes. We used Weighted Gene Co-expression Network Analysis (WGCNA) to cluster transcriptome-wide gene expression into modules. The gene expression profile of each module was then correlated with CO2 treatment levels (current-day: ~450 µatm, elevated: ~1,000 µatm) and visually-mediated behavioural responses previously shown to be altered at elevated CO2, using Canonical Correlation Analysis.
 
All statistical analyses were carried out in R (v4.0.4), primarily using RStudio (v 1.4.1106).
DESeq2 (v1.30.1) was used to normalise gene count data, remove low read counts and for variance stabilisation.
WGCNA (v1.70-3) was used for network construction and module detection.
CCA (v1.2.1) was used to explore the correlations between the two sets of variables from the same individual squid: set 1 = module eigengenes from each module representing the gene expression profile of the module, set 2 = CO2 level (current-day or elevated) and behavioural traits.
WGCNA (v1.70-3) was used to calculate module membership and gene significance to identify hub genes. clusterProfiler (v3.18.1) was used to run over-representation analysis using the hypergeometric test.
 
This data record contains:
1) All R code used for the statistical analyses (.html file)
2) Data files to accompany the statistical analyses = gene count data for the CNS and eyes of each individual squid (corset-counts.txt), CO2 treatment level and behavioural measurements for each individual squid (metadata.csv), explanation of each variable in metadata.csv (README.txt), annotated transcriptome assembly of Idiosepius pygmaeus CNS and eye tissues (annotated_transcriptome.csv), data linking each transcript from the transcriptome assembly to each gene in the gene count data (corset-clusters.txt)
 
Software/equipment used to manipulate/analyse the data: DESeq2 (v1.30.1)
WGCNA (v1.70-3)
CCA (v1.2.1)
clusterProfiler (v3.18.1)
Majority of analyses: Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)
WGCNA network construction and module detection: Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8 (Core)
 
The HTML file contains all R code used for the analyses, as well as the Session Information.
- Start
    Data Record Details
    Data record related to this publication Correlating gene expression profiles with CO2 treatment and OA-affected behaviours in the two-toned pygmy squid (Idiosepius pygmaeus)
    Data Publication title Correlating gene expression profiles with CO2 treatment and OA-affected behaviours in the two-toned pygmy squid (Idiosepius pygmaeus)
  • Description
    We correlated transcriptomic data from the central nervous system (CNS) and eyes of male two-toned pygmy squid (Idiosepius pygmaeus) with CO2 treatment levels and OA-affected behaviours in the same individuals to identify genes potentially contributing to OA-induced behavioural changes. We used Weighted Gene Co-expression Network Analysis (WGCNA) to cluster transcriptome-wide gene expression into modules. The gene expression profile of each module was then correlated with CO2 treatment levels (current-day: ~450 µatm, elevated: ~1,000 µatm) and visually-mediated behavioural responses previously shown to be altered at elevated CO2, using Canonical Correlation Analysis.
     
    All statistical analyses were carried out in R (v4.0.4), primarily using RStudio (v 1.4.1106).
    DESeq2 (v1.30.1) was used to normalise gene count data, remove low read counts and for variance stabilisation.
    WGCNA (v1.70-3) was used for network construction and module detection.
    CCA (v1.2.1) was used to explore the correlations between the two sets of variables from the same individual squid: set 1 = module eigengenes from each module representing the gene expression profile of the module, set 2 = CO2 level (current-day or elevated) and behavioural traits.
    WGCNA (v1.70-3) was used to calculate module membership and gene significance to identify hub genes. clusterProfiler (v3.18.1) was used to run over-representation analysis using the hypergeometric test.
     
    This data record contains:
    1) All R code used for the statistical analyses (.html file)
    2) Data files to accompany the statistical analyses = gene count data for the CNS and eyes of each individual squid (corset-counts.txt), CO2 treatment level and behavioural measurements for each individual squid (metadata.csv), explanation of each variable in metadata.csv (README.txt), annotated transcriptome assembly of Idiosepius pygmaeus CNS and eye tissues (annotated_transcriptome.csv), data linking each transcript from the transcriptome assembly to each gene in the gene count data (corset-clusters.txt)
     
    Software/equipment used to manipulate/analyse the data: DESeq2 (v1.30.1)
    WGCNA (v1.70-3)
    CCA (v1.2.1)
    clusterProfiler (v3.18.1)
    Majority of analyses: Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)
    WGCNA network construction and module detection: Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 8 (Core)
     
    The HTML file contains all R code used for the analyses, as well as the Session Information.
    •
  • Other Descriptors
    • Descriptor
      Additional data for analyses correlating gene expression profiles in the nervous system with CO2 treatment and OA-affected behaviours of the two-toned pygmy squid (Idiosepiud pygmaeus). All R code used for the statistical analyses, and data files to accompany the statistical analyses (raw gene count data, CO2 treatment level and behavioural measurements for each individual squid, annotated transcriptome assembly of Idiosepius pygmaeus CNS and eye tissues, data linking each transcript from the transcriptome assembly to each gene in the gene count data).
      •
      Descriptor type Brief
    • Data type dataset
  • Keywords
    • ocean acidification
    • carbon dioxide
    • transcriptomics
    • gene expression
    • central nervous system
    • eyes
    • squid
    • behaviour
    • Weighted Gene Co-expression Network Analysis
    • WGCNA
    • Canonical Correlation Analysis
    • neurobiological mechanisms
    • cephalopod
  • Funding source
    • ARC Centre of Excellence for Coral Reef Studies
    • Australian Government Research Training Program Scholarship
    • Okinawa Institute of Science and Technology & Graduate University
  • Research grant(s)/Scheme name(s)
    • -
    • Research themes
    Tropical Ecosystems, Conservation and Climate Change
    FoR Codes (*)
    SEO Codes
- Specify coverage
    Specify spatial or temporal setting of the data
    Temporal (time) coverage
  • Start Date 2019/08/20
  • End Date 2019/12/19
    • Time Period
    Spatial (location) coverage
  • Locations
    • 19°15'11"S 146°49'24"E
- Data
    Data Locations

    Type Location Notes
    Attachment corset-counts.txt Data file to accompany the statistical analysis. Gene count data for the CNS and eyes of each individual squid.
    Attachment metadata.csv Data file to accompany the staistical analysis. CO2 treatment level and behavioural measurements for each individual squid.
    Attachment README.txt Explanation of each variable in metadata.csv.
    Attachment corset-clusters.txt Data file to accompany the statistical analysis. Data linking each transcript from the transcriptome assembly to the corresponding gene in the gene count data ('Cluster-*').
    Attachment R_code_correlating_gene_expression_behaviour.html HTML with all R code used for statistical analyses.
    URL http://data.qld.edu.au/public/Q5842/2024-JodiThomas-83a8e1f098f711eca3e7bd90e4270a95-CorrelatingGeneExpression/ .csv file of the annotated transcriptome assembly of Idiosepius pygmaeus CNS and eye tissues.
    The Data Manager is: Philip Munday
    College or Centre ARC Centre of Excellence for Coral Reef Studies
    Access conditions Open: free access under license
  • Alternative access conditions
    • Data record size 7 files: 266.4 MB
- Related resources
  • Related publications
      Name Thomas, J. T., Spady, B. L., Munday, P. L. and Watson, S.-A. (2021). The role of ligand-gated chloride channels in behavioural alterations at elevated CO2 in a cephalopod. Journal of Experimental Biology 224, jeb242335.
    • URL https://doi.org/10.1242/jeb.242335
    • Notes Behavioural data from this publication was used for the analysis here.
  • Related websites
      Name
    • URL
    • Notes
  • Related metadata (including standards, codebooks, vocabularies, thesauri, ontologies)
      Name
    • URL
    • Notes
  • Related data
      Name
    • URL
    • Notes
  • Related services
      Name
    • URL
    • Notes
- License
- Citation
    Citation Thomas, Jodi; Huerlimann, Roger; Schunter, Celia; Watson, Sue-Ann; Munday, Philip; Ravasi, Timothy (2024): Correlating gene expression profiles with CO2 treatment and OA-affected behaviours in the two-toned pygmy squid (Idiosepius pygmaeus). James Cook University. https://doi.org/10.25903/7dcz-th66