Data from: The coral immune response facilitates protection against microbes during tissue regeneration

Data consists of 3 zip files:

(1) 16S rRNA amplicon sequencing - QIIME analysis: This archive file contains all input and output files required for and produced by the QIIME pipeline in the 'dataset' folder. The quality file Wound.qual and the sequence file Wound.fna along with the mapping files Map.txt and Map_corrected2.txt are the primary input files. Output files include the complete selection of OTU tables (otu_table.biom, Normalised_otu_table.biom as well the weighted and unweighted Unifrac tables). Additional special files required for analysis can be found in the 'input' folder. The script 'QIIME Analysis script.txt' was used for data analysis and the file 'Sample names.txt' should be used to determine the biological sample / treatment corresponding to each sample. Sequences have been deposited in the NCBI Sequence Read Archive (SRA) database under study accession number SRP052969.

(2) Immune parameter data: This archive file contains the data files for the expression levels of the range of immune parameters presented in the manuscript: 1) Chromoprotein expression levels, 2) Fluorescent protein expression levels, 3) Immune gene expression levels and 4) PO and tpPO activity levels. Each file contains a description of the samples and sample names used.

(3) Fluorescent Protein Analysis Methodology: This archive file contains the files required for the fluorescent protein spectral analysis. The input file Wounding_Aaspera_fl.csv containing the raw fluorescence values and sample protein concentration is provided along with the reference fluorescent protein data file modelspecs_interp_25sh.csv (based on the spectrum of purified Acropora millepora fluorescent proteins) and the spectral decomposition script specs_regression_WF.R. The reference fluorescent protein data and the script were provided by Mikhail Matz.

Abstract [Related Publication]: Increasing physical damage on coral reefs from predation, storms and anthropogenic disturbances highlights the need to understand the impact of injury on the coral immune system. In this study, we examined the regulation of the coral immune response over 10 days following physical trauma artificially inflicted on in situ colonies of the coral Acropora aspera, simultaneously with bacterial colonization of the lesions. Corals responded to injury by increasing the expression of immune system-related genes involved in the Toll-like and NOD-like receptor signalling pathways and the lectin–complement system in three phases (<2, 4 and 10 days post-injury). Phenoloxidase activity was also significantly upregulated in two phases (

The full methodology is available in the publication shown in the Related Publications link below.

    Data Record Details
    Data record related to this publication Data from: The coral immune response facilitates protection against microbes during tissue regeneration
    Data Publication title Data from: The coral immune response facilitates protection against microbes during tissue regeneration
  • Description

    Data consists of 3 zip files:

    (1) 16S rRNA amplicon sequencing - QIIME analysis: This archive file contains all input and output files required for and produced by the QIIME pipeline in the 'dataset' folder. The quality file Wound.qual and the sequence file Wound.fna along with the mapping files Map.txt and Map_corrected2.txt are the primary input files. Output files include the complete selection of OTU tables (otu_table.biom, Normalised_otu_table.biom as well the weighted and unweighted Unifrac tables). Additional special files required for analysis can be found in the 'input' folder. The script 'QIIME Analysis script.txt' was used for data analysis and the file 'Sample names.txt' should be used to determine the biological sample / treatment corresponding to each sample. Sequences have been deposited in the NCBI Sequence Read Archive (SRA) database under study accession number SRP052969.

    (2) Immune parameter data: This archive file contains the data files for the expression levels of the range of immune parameters presented in the manuscript: 1) Chromoprotein expression levels, 2) Fluorescent protein expression levels, 3) Immune gene expression levels and 4) PO and tpPO activity levels. Each file contains a description of the samples and sample names used.

    (3) Fluorescent Protein Analysis Methodology: This archive file contains the files required for the fluorescent protein spectral analysis. The input file Wounding_Aaspera_fl.csv containing the raw fluorescence values and sample protein concentration is provided along with the reference fluorescent protein data file modelspecs_interp_25sh.csv (based on the spectrum of purified Acropora millepora fluorescent proteins) and the spectral decomposition script specs_regression_WF.R. The reference fluorescent protein data and the script were provided by Mikhail Matz.

    Abstract [Related Publication]: Increasing physical damage on coral reefs from predation, storms and anthropogenic disturbances highlights the need to understand the impact of injury on the coral immune system. In this study, we examined the regulation of the coral immune response over 10 days following physical trauma artificially inflicted on in situ colonies of the coral Acropora aspera, simultaneously with bacterial colonization of the lesions. Corals responded to injury by increasing the expression of immune system-related genes involved in the Toll-like and NOD-like receptor signalling pathways and the lectin–complement system in three phases (<2, 4 and 10 days post-injury). Phenoloxidase activity was also significantly upregulated in two phases (

    The full methodology is available in the publication shown in the Related Publications link below.

  • Other Descriptors
    • Descriptor

      This dataset is available from Dryad. Dryad data package: van de Water JAJM, Ainsworth TD, Leggat W, Bourne DG, Matz MV, Willis BL, van Oppen MJH (2015) Data from: The coral immune response facilitates protection against microbes during tissue regeneration. Dryad Digital Repository. https://doi.org/10.5061/dryad.r24b1

    • Descriptor type Note
  • Data type dataset
  • Keywords
    • coral
    • immunity
    • bacteria
    • injury
    • gene expression
    • ARC Centre of Excellence for Coral Reef Studies
  • Funding source
  • Research grant(s)/Scheme name(s)
  • Research themes
    Tropical Ecosystems, Conservation and Climate Change
    FoR Codes (*)
    • 060205 - Marine and Estuarine Ecology (incl. Marine Ichthyology)
    SEO Codes
    • 960808 - Marine Flora, Fauna and Biodiversity
    Specify spatial or temporal setting of the data
    Temporal (time) coverage
  • Start Date
  • End Date
  • Time Period
    Spatial (location) coverage
  • Locations
    • Samples collected from the reef flat of Heron Island, Great Barrier Reef, Australia (23°26′31.20″S, 151°54′50.40″E)
    Data Locations

    Type Location Notes
    URL https://doi.org/10.5061/dryad.r24b1
    The Data Manager is: Johannes van de Water
    College or Centre
    Access conditions Open: free access under license
  • Alternative access conditions
  • Data record size 3 zip files: 768.86 KB
  • Related publications
      Name van de Water, A.J.M., Ainsworth, Tracy D., Leggat, William, Bourne, David G., Willis, Bette L., and Van Oppen, Madeleine J.H. (2015) The coral immune response facilitates protection against microbes during tissue regeneration. Molecular Ecology, 24 (13). pp. 3390-3404.
    • URL http://dx.doi.org/10.1111/mec.13257
    • Notes
  • Related websites
      Name
    • URL
    • Notes
  • Related metadata (including standards, codebooks, vocabularies, thesauri, ontologies)
  • Related data
  • Related services
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    • URL
    • Notes
    Citation van de Water, Johannes; Ainsworth, Tracy; Leggat, William; Willis, Bette; van Oppen, Madeleine; Bourne, D; Matz, M (2015): Data from: The coral immune response facilitates protection against microbes during tissue regeneration. James Cook University.