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RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)
Citatie
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 https://doi.org/10.15468/9ya44h
Contact: Alcamí, Antonio
Toegang tot data
Gearchiveerde data
Beschikbaarheid: Creative Commons License Deze dataset valt onder een Creative Commons Naamsvermelding 4.0 Internationaal-licentie.
Beschrijving
RNA shotgun sequencing (454 pyrosequencing) metagenome dataset of viruses in lake Limnopolar (Livingston Island, Antarctica), over a three-year period. meer

Samples were taken aseptically.
Study Extent: 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.
Method step description:
  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).
Scope
Kernwoorden:
Zoet water, Metadata, Rna viruses, Antarctica, South Shetland I., Livingston I., Viruses
Geografische spreiding
Antarctica, South Shetland I., Livingston I. Stations [Marine Regions]
Limnopolar lake
Spreiding in de tijd
27 November 2007 - 1 Februari 2010
Taxonomic coverage
Viruses [WoRMS]
Parameter
Moleculaire data
Bijdrage door
Universidad Autónoma de Madrid, meer, data creator
Lopez-Bueno, Alberto
Rastrojo, Alberto
Peiro, Ramon
Arenas, M.
Alcamí, Antonio
Gerelateerde datasets
Gepubliceerd in:
AntOBIS: Antarctic Ocean Biodiversity Information System, meer
(Gedeeltelijk) opgenomen in:
RAS: Register of Antarctic Species, meer
Dataset status: Afgelopen
Data type: Meta database
Data oorsprong: Onderzoek: veldonderzoek
Metadatarecord aangemaakt: 2019-04-08
Informatie laatst gewijzigd: 2019-04-10
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