Research Data

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

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General
Title
Data from: The coral immune response facilitates protection against microbes during tissue regeneration
Type
Dataset
Date Record Created
2017-11-27
Date Record Modified
2018-01-02
Language
English
Coverage
Date Coverage
(no information)
Time Period
(no information)
Geospatial Location
  • Samples collected from the reef flat of Heron Island, Great Barrier Reef, Australia (23°26′31.20″S, 151°54′50.40″E)
Description
Descriptions
  1. Type: full

    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.

  2. Type: note

    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

Related Publications
  1. 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.
Related Websites
(no information)
Related Data
  1. Has association with: >> Acropora aspera metagenome
    • ID: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA273783 (EXTERNAL)
    • Note(s): BioProject PRJNA273783 submitted by Australian Insitute of Marine Science
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
Related Services
(no information)
Technical metadata
(no information)
People
Creators
  1. Managed by: Mr Johannes van de Water , jeroen.vandewater@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies
  2. Associated with: Dr Tracy Ainsworth , tracy.ainsworth@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Molecular and Cell Biology
  3. Associated with: A/Prof William Leggat , bill.leggat@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, College of Science & Engineering, Comparative Genomics Centre
  4. Associated with: Prof Bette Willis , bette.willis@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Marine Biology & Aquaculture
  5. Associated with: Dr Madeleine van Oppen , madeleine.vanoppen@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Molecular and Cell Biology
Primary Contact
Mr Johannes van de Water, jeroen.vandewater@jcu.edu.au
Supervisors
(no information)
Collaborators
  1. David G. Bourne, AIMS@JCU and Australian Institute of Marine Science, Townsville, Queensland, Australia
  2. Mikhail Matz, University of Texas at Austin, USA
Subject
Fields of Research
  1. 060205 - Marine and Estuarine Ecology (incl. Marine Ichthyology) (060205)
Socio-Economic Objective
  1. 960808 - Marine Flora, Fauna and Biodiversity (960808)
Keywords
  1. coral
  2. immunity
  3. bacteria
  4. injury
  5. gene expression
  6. ARC Centre of Excellence for Coral Reef Studies
Research Activity
(no information)
Research Themes
Tropical Ecosystems, Conservation and Climate Change
Rights
License
(no information)
License - Other
CC 0: Public Domain Dedication 1.0 Universal
Access Rights/Conditions
Open access. If the data is not feely accessible via the link provided, please contact the nominated data manager or researchdata@jcu.edu.au for assistance.
Type
open
Rights
(no information)
Data
Data Location
Online Locations
  1. https://doi.org/10.5061/dryad.r24b1
Stored At
(no information)
Citation
Cite:
van de Water, J.; Ainsworth, T.; Leggat, W.; Bourne, D.; Matz, M.; Willis, B.; van Oppen, M. (2015). Data from: The coral immune response facilitates protection against microbes during tissue regeneration. James Cook University. (dataset). 2cf0c37c59bf28036fa3187277ce27c5