Data

Great Barrier Reef Genomics Database: Seawater Illumina Reads

Australian Institute of Marine Science
Australian Institute of Marine Science (AIMS)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
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While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.&rft_rights=Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: Australian Institute of Marine Science (AIMS). (2022). Great Barrier Reef Genomics Database: Seawater Illumina Reads. https://doi.org/10.25845/Q4XH-YN10, accessed[date-of-access].&rft_subject=oceans&rft_subject=diver&rft_subject=Microbial Genomic Database Sub-Facility, Integrated Marine Observing System (IMOS)&rft_subject=Turbidity of the water body&rft_subject=Fluorescence of the water body&rft_subject=Concentration of nitrate {NO3} per unit volume of the water body&rft_subject=Practical salinity of the water body&rft_subject=Concentration of chlorophyll per unit volume of the water body&rft_subject=Concentration of pheophytin-a per unit volume of the water body&rft_subject=Concentration of phosphate {PO4} per unit volume of the water body&rft_subject=Concentration of suspended particulate material per unit volume of the water body&rft_subject=Concentration of dissolved nitrite per unit volume of the water body&rft_subject=Concentration of ammonium {NH4} per unit volume of the water body&rft_subject=Temperature of the water body&rft_subject=Concentration of total dissolved phosphorus {TDP} per unit volume of the water body&rft.type=dataset&rft.language=English Access the data
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Creative Commons Attribution 3.0 Australia License
http://creativecommons.org/licenses/by/3.0/au/

Use Limitation: All AIMS data, products and services are provided "as is" and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.

Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "Australian Institute of Marine Science (AIMS). (2022). Great Barrier Reef Genomics Database: Seawater Illumina Reads. https://doi.org/10.25845/Q4XH-YN10, accessed[date-of-access]".

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Brief description

This dataset comprises of microbial metagenomics sequencing reads of seawater collected across 48 reef sites across the Great Barrier Reef. Samples were collected across four Long Term Monitoring Program (LTMP) field trips between November 2019-July 2020, combining water chemistry data, LTMP field surveys and microbial metagenomics data. This data collection was a major part of the QRCIF IMOS GBR microbial genomic database project, which aims to generate a comprehensive open access repositor of microbial genomic data from across the region. Seawater was collected in quadruplicate either by SCUBA or using Niskin Bottles at each reef site, 5L of seawater was pre-filtered using a 5µm filter and applied to a 0.22µm sterivex filter, snap frozen and stored at -20°C in preparation of DNA extraction. DNA was extracted from sterivex filters using phenol:chloroform:Iso-amyl alcolol extraction, ethanol precipitation and cleanup using the Zymo Clean and Concentrator® kit before submission for sequencing at the Australian Centre for Ecogenomics sequencing facility, Illumina. The data presented as illumina paired-end shotgun metagenomics sequencing runs, in fastq format, generated by Microba Life Sciences, Brisbane, QLD, Australia. Each downloadable archive contains forward and reverse reads for all replicate sampling performed at that particular site. Water quality particulate and dissolved nutrient data was generated as previously described (https://doi.org/10.25845/5c09b551f315b) from water samples collected simultaneously at each reef site. Zip files are available through the spatial layer under each site's 'illumina.seawater.zip' - please note these are large downloads (between 6 - 14 GB).

Lineage

Maintenance and Update Frequency: notPlanned
Statement: Water quality particulate and dissolved nutrient data was generated as previously described https://doi.org/10.25845/5c09b551f315b Water quality chlorophyll and turbidity measurements was generated as previously described https://doi.org/10.25845/CMVM-ZT18 Underway Sensors: Enhanced Measurements From Ships Of Opportunity (SOOP)https://apps.aims.gov.au/metadata/view/8af21108-c535-43bf-8dab-c1f45a26088c Underway data were collected throughout the trips and data assembled here are displayed with closest 'Sample Collection Start' times (i.e. <10mins difference), except in two instances, ship sensor readings >30mins time difference occurs (Helix Reef and 21-550 Reef).

Notes

Credit
Yeoh, YK. AIMS, Australia
Credit
GBR Microbial Genomic Database project is funded by the Department of Environment and Science, Research Infrastructure Co-investment Fund (RICF) in partnership with Australian Institute of Marine Science (AIMS), Integrated Marine Observing System (IMOS) and University of Queensland
Credit
Webster, NS. Australian Antarctic Program, Australia; Australian Centre for Ecogenomics, UQ, Australia; AIMS, Australia
Credit
Hugenholtz, P. Australian Centre for Ecogenomics, University of Queensland (UQ), Australia
Credit
Robbins, S. Australian Centre for Ecogenomics,UQ, Australia
Credit
Australia’s Integrated Marine Observing System (IMOS) is enabled by the National Collaborative Research Infrastructure Strategy (NCRIS). It is operated by a consortium of institutions as an unincorporated joint venture, with the University of Tasmania as Lead Agent.
Credit
Laffy, PW. Australian Institute of Marine Science (AIMS), Australia
Credit
Bell, SC. AIMS, Australia
Credit
Terzin, M. AIMS, Australia, JCU, Australia
Credit
Bourne, DG. James Cook University (JCU), Australia; AIMS, Australia

Modified: 17 10 2024

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Subjects
Concentration of ammonium {NH4} per unit volume of the water body | Concentration of chlorophyll per unit volume of the water body | Concentration of dissolved nitrite per unit volume of the water body | Concentration of nitrate {NO3} per unit volume of the water body | Concentration of pheophytin-a per unit volume of the water body | Concentration of phosphate {PO4} per unit volume of the water body | Concentration of suspended particulate material per unit volume of the water body | Concentration of total dissolved phosphorus {TDP} per unit volume of the water body | Fluorescence of the water body | Microbial Genomic Database Sub-Facility, Integrated Marine Observing System (IMOS) | Practical salinity of the water body | Temperature of the water body | Turbidity of the water body | diver | oceans |

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Other Information
Data Dictionary - GBR Genomics Database: Seawater Illumina Reads

uri : https://api.aims.gov.au/data-v2.0/5956fd44-f864-4811-9ec3-15499f1863c4/files/Data-Dictionary_GBR-Genomics-Database_Seawater-Illumina-Reads.docx

GeoPackage GBR Genomics Database - Seawater Illumina Reads [gpkg size: 132KB]

uri : https://api.aims.gov.au/data-v2.0/5956fd44-f864-4811-9ec3-15499f1863c4/files/GBR-Genomics-Database_Seawater-Illumina-Reads.gpkg

GBR Genomics Database - Seawater Illumina Reads [csv file size: 23KB]

uri : https://api.aims.gov.au/data-v2.0/5956fd44-f864-4811-9ec3-15499f1863c4/files/GBR-Genomics-Database_Seawater-Illumina-Reads.csv

Identifiers
  • global : 5956fd44-f864-4811-9ec3-15499f1863c4
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