virome_antarctic_lakes_2010
最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 2021年6月17日 SCAR - Microbial Antarctic Resource System

Virome dataset based on shotgun 454 sequencing of virus-concentrated samples from lakes in the Antarctic Peninsula (2010).

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de Carcer D A, Lopez-Bueno A, Alonso-Lobo J, Quesada A, Alcami A (2021): virome_antarctic_lakes_2010. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=virome_antarctic_lakes_2010&v=1.0

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此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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關鍵字

Metadata

聯絡資訊

資源建立者:

Daniel Aguire de Carcer
Universidad Autónoma de Madrid
Madrid
ES
Alberto Lopez-Bueno
Universidad Autónoma de Madrid
Madrid
ES
Juan Alonso-Lobo
Universidad Autónoma de Madrid
Madrid
ES
Antonio Quesada
Universidad Autónoma de Madrid
Madrid
ES
Antonio Alcami
Universidad Autónoma de Madrid
Madrid
ES

可回覆此資源相關問題者:

Antonio Alcami
Universidad Autónoma de Madrid
Madrid
ES

元數據填寫者:

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences
Brussels
BE

與此資源的相關者:

使用者
Antonio Alcami
Universidad Autónoma de Madrid
Madrid
ES
地理涵蓋範圍

Antarctic Peninsula: Caleta Cierva, Avian Island, Green Island, Pourquoi Pas Island and Livingston Island (South Shetland Islands)

界定座標範圍 緯度南界 經度西界 [-67.46, -68.54], 緯度北界 經度東界 [-62.38, -60.58]
時間涵蓋範圍
起始日期 / 結束日期 2010-01-21 / 2010-01-28
計畫資料

無相關描述

計畫名稱 virome_antarctic_lakes_2010
經費來源 "Análisis metagenómico de las comunidades virales de 7 lagos de la Antártida" (Grant ID CTM2009-08644-E, Spanish Polar Programme and the Spanish Ministry of Economy and Competitiviness)

參與計畫的人員:

Antonio Alcami
取樣方法

Water samples were preserved at 4°C and viral particles purified within the first 24 h of sampling. From each water body, 60–90 l were first filtered through a 30 μm nylon mesh to remove large particles, and then by tangential flow filtration (TFF) using a peristaltic pump coupled to a Centramate holder (Pall) with two cassettes of 0.45 μm (2 × 0.019 m2, PES) to remove bacteria and smaller eukaryotes.

研究範圍 Samples were taken from several freshwater bodies in the Antarctic Peninsula during the Austral summer 2010.

方法步驟描述:

  1. The filtrated viral fraction was concentrated 100 times by TFF with two cassettes of 70 kDa exclusion size at pressures below 10 p.s.i., in order to maintain viral particle integrity. Viral stocks were preserved at −20°C for transportation, and finally stored at −80°C before subsequent processing. All material was acid-rinsed (0.1 N HCl) and extensively washed with Milli Q or 70 kDa-filtered lake water.
  2. Frozen stocks were thawed at 4°C with gentle rocking, and then passed through a 25% sucrose cushion by centrifugation for 16 h at 60 000 g and 4°C. The resulting pellets were resuspended in TE buffer (10 mM Tris pH 8, 1 mM EDTA), and filtered using a sterile 0.45 μm syringe filter. Viral concentrates were then treated with DNAse I (500 U ml−1), Nuclease S7 (500 U ml−1), RNAse A (100 μg ml−1) and RNAse H (2 U per reaction) for 30 min at room temperature to remove free nucleic acids. Nuclease reactions were stopped with EDTA and EGTA (12 and 2 mM, respectively), and viral capsids and envelopes were then disrupted with SDS (0.5%) and proteinase K (200 μg ml−1) treatment.
  3. Viral DNA was extracted with phenol–chloroform, ethanol precipitated and randomly amplified using Phi29 polymerase and modified random hexamers (GenomiPhi HY, GE Healthcare) for 2.5 h, according to the manufacturer's instructions. The samples were subsequently shot-gun sequenced with a Roche 454 FLX sequencer (Parque Científico de Madrid).
引用文獻
  1. de Cárcer A. D., López-Bueno A., Alonso-Lobo J. M., Quesada A., & Alcamí A. (2016). Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula. FEMS microbiology ecology, 92(6), fiw074.
額外的元數據