Metagenome assembly of an Amundsen Sea (Antarctica, Southern Ocean) water sample

Versão mais recente published by SCAR - Microbial Antarctic Resource System on mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de Março de 2019
Licença:
CC-BY 4.0

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Descrição

Seven assembled metagenoms from a metagenomic sequencing (Illumina HiSeq; paired-end) sample taken during a phytoplankton bloom in the Amundsen Sea (Antarctica, Southern Ocean)

Versões

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

Metadata

Contatos

Tom Delmont
  • Originador
  • Ponto De Contato
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Murat Eren
  • Originador
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Joseph Veneis
  • Originador
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Anton Post
  • Originador
University of Rhode Island
Narragansett
US
Maxime Sweetlove
  • Provedor Dos Metadados
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels
BE

Cobertura Geográfica

Amundsen Sea, Southern Ocean

Coordenadas delimitadoras Sul Oeste [-73,342, -112,401], Norte Leste [-73,342, -112,401]

Cobertura Temporal

Data Inicial 2010-12-19

Dados Sobre o Projeto

Nenhuma descrição disponível

Título ASPIRE Microbiome
Financiamento This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095.

O pessoal envolvido no projeto:

Anton Post

Métodos de Amostragem

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.

Área de Estudo Water samples were taken with a CTD Rosette equipped during a phytoplankton bloom event in the ASP in 2010–2011.

Descrição dos passos do método:

  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).

Citações bibliográficas

  1. 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.

Metadados Adicionais

Identificadores alternativos 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2
https://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome