元數據

RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 2019年3月26日 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月26日
授權條款:
CC-BY 4.0

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說明

RNA shotgun sequencing (454 pyrosequencing) metagenome dataset of viruses in lake Limnopolar (Livingston Island, Antarctica), over a three-year period.

版本

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如何引用

研究者應依照以下指示引用此資源。:

Lopez-Bueno A, Rastrojo A, Peiro R, Arenas M, Alcami A (2019): RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica). v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=virome_livingston_island_antarctica&v=1.0

權利

研究者應尊重以下權利聲明。:

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.

GBIF 註冊

此資源已向GBIF註冊,並指定以下之GBIF UUID: 9b846f85-327e-412d-abb7-2eef49b6fae4。  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:
-

A. Lopez-Bueno
Universidad Autónoma de Madrid
Madrid
ES
A. Rastrojo
Universidad Autónoma de Madrid
Madrid
ES
R. Peiro
Universidad Autónoma de Madrid
Madrid
ES
M. Arenas
Universidad Autónoma de Madrid
Madrid
ES
A. Alcami
Universidad Autónoma de Madrid
Madrid
ES

可回覆此資源相關問題者:

A. Alcami
Universidad Autónoma de Madrid
Madrid
ES

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

Limnopolar lake, Livingston Island, South Shetland Islands, Antarctica

界定座標範圍 緯度南界 經度西界 [-62.38, -61.06], 緯度北界 經度東界 [-62.38, -61.06]

分類群涵蓋範圍

RNA-Viruses targeted with RNA-shotgun sequencing (454 pyrosequencing)

時間涵蓋範圍

起始日期 / 結束日期 2007-11-27 / 2010-02-01

計畫資料

無相關描述

計畫名稱 RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)
經費來源 This project was funded by the Spanish Polar Programme and the Spanish Ministry of Economy and Competitiveness (CTM2008‐05134‐E/ANT and CTM2009‐08644‐E).

參與計畫的人員:

A. Alcami

取樣方法

Samples were taken aseptically.

研究範圍 Lake Limnopolar (Livingston Island, Antarctica) was sampled for cyanobacteria mats on the 27th of November 2006, the 22nd of January 2007 and the 1st of February 2010.

方法步驟描述:

  1. Cyanobacterial mat samples (2.5 g) were homogenized in SM buffer (50 mm Tris‐HCl pH 7.5, 100 mm NaCl and 8 mm MgSO4.7H2O) by three cycles of vigorous vortex and sonication in a water bath during 20 and 10 s, respectively, then centrifuged at 3000 g for 5 min. This process was repeated twice. The resulting supernatants were combined and centrifuged at 8000 g for 1 h and then filtered through a 0.45‐μm syringe filter (Millex, Durapore PVDF) to remove cellular organisms. The resulting viral fractions, as well as those from lake water samples, were purified as described previously (López‐Bueno et al. 2009). In the case of the water sample collected in 2010, 0.45 μm filtration was carried out by TFF using two 0.093 m2 polyethersulfone filter cassettes (Pall) and nuclease treatment of purified viral particles included 100 U/mL of nuclease S7 (Roche). RNA viral genomes were purified with Trizol‐LS (Invitrogen) followed by DNAseI RNAse‐free (Roche) treatment before randomly amplification by sequence independent single primer amplification (SISPA) (Victoria et al. 2008; Djikeng et al. 2009; Culley et al. 2010). Briefly, Superscript II or III and the Klenow fragment (3′–>5′exo‐) enzyme (NEBiolabs) were used to convert RNA into dsDNA using 60 pmol of pseudo‐degenerated primers FR26‐RV (5′‐GCCGGAGCTCTGCAGATATCNNNNNN‐3) for the water sample collected in 2007 and primer A (5′‐GTTTCCCAGTCACGATANNNNNNNNN‐3) for samples collected in 2006 and 2010. After 40 cycles of PCR amplification with FastStart high fidelity polymerase (Roche), DNA fragments between 500 and 3000 bp were gel‐extracted with QIAquick Gel Extraction kit (Qiagen) and sequenced in the 454 GS FLX titanium platforms (Roche‐454) from LifeSequencing (Valencia, Spain) or from Parque Científico de Madrid (Spain).

引用文獻

  1. López‐Bueno, A., Rastrojo, A., Peiró, R., Arenas, M., & Alcamí, A. (2015). Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Molecular ecology, 24(19), 4812-4825. https://doi.org/10.1111/mec.13321