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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

Access data
Archived data
Availability: Creative Commons License 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:
  1. 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).
  2. 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, moredata creator

Related datasets
Published in:
AntOBIS: Antarctic Ocean Biodiversity Information System, more
(Partly) included in:
RAS: Register of Antarctic Species, more

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-03
Information last updated: 2019-04-11
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy