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

Versão mais recente publicado por SCAR - Microbial Antarctic Resource System em 26 de Março de 2019 SCAR - Microbial Antarctic Resource System
Publication date:
26 de Março de 2019
License:
CC-BY 4.0

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Descrição

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

Versões

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

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: 9b846f85-327e-412d-abb7-2eef49b6fae4.  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

Quem criou esse recurso:
-

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

Quem pode responder a perguntas sobre o recurso:

A. Alcami
Universidad Autónoma de Madrid
Madrid
ES

Quem preencher os metadados:
-

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

Quem mais foi associado com o recurso:

Usuário

Cobertura Geográfica

Limnopolar lake, Livingston Island, South Shetland Islands, Antarctica

Coordenadas delimitadoras Sul Oeste [-62,38, -61,06], Norte Leste [-62,38, -61,06]

Cobertura Taxonômica

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

Cobertura Temporal

Data Inicial / Data final 2007-11-27 / 2010-02-01

Dados Sobre o Projeto

Nenhuma descrição disponível

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

O pessoal envolvido no projeto:

A. Alcami

Métodos de Amostragem

Samples were taken aseptically.

Área de Estudo 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.

Descrição dos passos do método:

  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).

Citações bibliográficas

  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

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