Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample
Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019
Seven assembled metagenoms from a metagenomic sequencing (Illumina HiSeq; paired-end) sample taken during a phytoplankton bloom in the Amundsen Sea (Antarctica, Southern Ocean)
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Delmont T, Eren M, Veneis J, Post A (2019): Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome&v=1.1
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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.
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Geographic Coverage
Amundsen Sea, Southern Ocean
| Bounding Coordinates | South West [-73.342, -112.401], North East [-73.342, -112.401] |
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Temporal Coverage
| Start Date | 2010-12-19 |
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Project Data
No Description available
| Title | ASPIRE Microbiome |
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| Funding | This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095. |
The personnel involved in the project:
Sampling Methods
A sample was taken from the surface water layer in the center of a bloom (073° 34′243S 112° 40′080W, chlorophyll a > 17 μg/L, temperature of −1.2°C, phosphate: 1.31 μM, nitrite: 0.02 μM, ammonium: 0.05 μM, silicate: 77.8 μM) on 19 December 2010. This sample (6 l, 10 m depth) was passed over a 20 μm mesh, collected onto a 0.2 μm Sterivex membrane filter cartridge by pressure filtration, quickly frozen in the headspace of a LN2 dewar and stored at −80°C.
| Study Extent | Water samples were taken with a CTD Rosette equipped during a phytoplankton bloom event in the ASP in 2010–2011. |
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Method step description:
- DNA extraction was performed using the Puregene kit (Gentra) after disruption of the cells with lytic enzyme coupled to proteinase K (Sinigalliano et al., 2007). DNA was quantified using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Wilmington, DE).
- Metagenomic libraries were generated with the OVATION ultralow kit (NuGen) using 100 ng of DNA and 8 amplification cycles. We constructed overlapping (2X100 nt with ~40 nt of overlap) and gapped (2X108 nt with an insert size of ~600 nt) metagenomic DNA libraries using a Pippin prep electrophoresis platform to precisely select the desired length for DNA fragments to be used for sequencing on a Hiseq platform (Illumina).
Bibliographic Citations
- Delmont, T. O., Eren, A. M., Vineis, J. H., & Post, A. F. (2015). Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Frontiers in microbiology, 6, 1090.
Additional Metadata
| Alternative Identifiers | 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2 |
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| https://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome |