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Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample
Citation
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 https://doi.org/10.15468/9yfu4e
Contact:
Delmont, Tom
Availability: This dataset is licensed under a Creative Commons Attribution 4.0 International License.
Description
Seven assembled metagenoms from a metagenomic sequencing (Illumina HiSeq; paired-end) sample taken during a phytoplankton bloom in the Amundsen Sea (Antarctica, Southern Ocean). more
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.
Method step description:
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.
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).
Scope
Themes:
Biology > Plankton > Phytoplankton
Keywords:
Marine/Coastal, Algal blooms, Dna sequencing, Metadata, PSW, Amundsen Sea
Geographical coverage
PSW, Amundsen Sea
Temporal coverage
2010 - 2011
Parameter
Molecular data
Contributors
Marine Biological Laboratory; The Josephine Bay Paul Center in Camparative Molecular Biology and Evolution, more, data creator
Delmont, Tom
Eren, Murat
Veneis, Joseph
Post, Anton
Eren, Murat
Veneis, Joseph
Post, Anton
Related datasets
Published in:
AntOBIS: Antarctic Ocean Biodiversity Information System
(Partly) included in:
RAS: Register of Antarctic Species
Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-03
Information last updated: 2019-04-11