virome_antarctic_lakes_2010
Versão mais recente publicado por SCAR - Microbial Antarctic Resource System em 17 de Junho de 2021 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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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

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: 9c226382-bbf8-420c-bfcc-bb417be1f181.  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.

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Metadata

Contatos

Quem criou esse recurso:

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

Quem pode responder a perguntas sobre o recurso:

Antonio Alcami
Universidad Autónoma de Madrid
Madrid
ES

Quem preencher os metadados:

Maxime Sweetlove
Royal Belgian Institute of Natural Sciences
Brussels
BE

Quem mais foi associado com o recurso:

Usuário
Antonio Alcami
Universidad Autónoma de Madrid
Madrid
ES
Cobertura Geográfica

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

Coordenadas delimitadoras Sul Oeste [-67,46, -68,54], Norte Leste [-62,38, -60,58]
Cobertura Temporal
Data Inicial / Data final 2010-01-21 / 2010-01-28
Dados Sobre o Projeto

Nenhuma descrição disponível

Título virome_antarctic_lakes_2010
Financiamento "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)

O pessoal envolvido no projeto:

Antonio Alcami
Métodos de Amostragem

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.

Área de Estudo Samples were taken from several freshwater bodies in the Antarctic Peninsula during the Austral summer 2010.

Descrição dos passos do método:

  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).
Citações bibliográficas
  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.
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