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

版本 1.0 由 SCAR - Microbial Antarctic Resource System 發佈於 Feb 4, 2019 SCAR - Microbial Antarctic Resource System

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. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=amundsen_sea_metagenome&v=1.0

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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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此資源已向GBIF註冊，並指定以下之GBIF UUID: 4f0d3a6f-c91e-4db9-a2f3-6a6007e620e2。  SCAR - Microbial Antarctic Resource System 發佈此資源，並經由Scientific Committee on Antarctic Research同意向GBIF註冊成為資料發佈者。

關鍵字

Metadata

聯絡資訊

資源建立者:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Murat Eren
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Joseph Veneis
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Anton Post
University of Rhode Island Narragansett US

可回覆此資源相關問題者:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

與此資源的相關者:

使用者

地理涵蓋範圍

Amundsen Sea, Southern Ocean

界定座標範圍 緯度南界 經度西界 [-73.342, -112.401], 緯度北界 經度東界 [-73.342, -112.401]

時間涵蓋範圍

起始日期 2010-12-19

計畫資料

無相關描述

計畫名稱 ASPIRE Microbiome
經費來源 This work was performed with financial support from NSF Antarctic Sciences awards ANT-1142095.

The personnel involved in the project:

Anton Post

取樣方法

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.

研究範圍 Water samples were taken with a CTD Rosette equipped during a phytoplankton bloom event in the ASP in 2010–2011.

方法步驟描述:

  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).

引用文獻

  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.