說明
Virome dataset based on shotgun 454 sequencing of virus-concentrated samples from lakes in the Antarctic Peninsula (2010).
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。:
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
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: 9c226382-bbf8-420c-bfcc-bb417be1f181。 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
- 出處
- 出處
- 出處
- 出處
- 出處 ●
- 使用者 ●
- 連絡人
- 元數據提供者
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] |
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時間涵蓋範圍
| 起始日期 / 結束日期 | 2010-01-21 / 2010-01-28 |
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計畫資料
無相關描述
| 計畫名稱 | virome_antarctic_lakes_2010 |
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| 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:
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. |
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方法步驟描述:
- 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.
- 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.
- 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
- 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.