元數據

Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 2019年3月19日 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
授權條款:
CC-BY 4.0

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說明

Amplicon sequencing dataset of microbial eukaryotes (18S ssh rRNA v4)living in the plankton of the Southern Ocean around the Western Antarctic Peninsula. Samples were collected during the annual Palmer LTER cruise from Jan to early Feb in 2014 aboard the R/V Laurence M. Gould.

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。:

Lin Y, Cassar N, Marchetti A, Moreno C, Ducklow H, Li Z (2018): Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton. v1.3. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=palmer_lter_eukaryote_18s_plankton&v=1.3

權利

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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: fd933a3c-e0a9-4c18-8e95-d1128a2be2ca。  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:
-

Yajuan Lin
Duke University
Durham
US
Nicolas Cassar
Duke University
Durham
US
Adrian Marchetti
University of North Carolina at Chapel Hill
Chapel Hill
US
Carly Moreno
University of North Carolina at Chapel Hill
Chapel Hill
US
Hugh Ducklow
Columbia University
Palisades
US
Zuchuan Li
Duke University
Durham
US

可回覆此資源相關問題者:

Yajuan Lin
Duke University
Durham
US

元數據填寫者:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute for 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

Southern Ocean around the Western Antarctic Peninsula.

界定座標範圍 緯度南界 經度西界 [-68.287, -74.184], 緯度北界 經度東界 [-63.965, -63.403]

分類群涵蓋範圍

microbial eukaryote plankton (18S ssh rRNA gene v4 region)

Domain Eukaryota (Eukaryotes)

計畫資料

無相關描述

計畫名稱 LTER_2014
經費來源 This work was supported by NSF OPP-1043339, NSF PLR-1440435 (Palmer LTER), NSF OPP-1341479, the “Laboratoire d’Excellence” LabexMER (ANR-10-LABX-19) and co-funded by a grant from the French government under the program “Investissements d’Avenir”.

參與計畫的人員:

Yajuan Li
Nicolas Cassar

取樣方法

Surface seawater from the vessel seawater supply line was gently vacuum filtered through a 0.2 µm pore size Millipore Supor filters. Each filter was then preserved immediately in 1 ml of RNA-later and stored at −80 °C.

研究範圍 Samples were taken during the annual Palmer LTER cruise from Jan to early Feb in 2014 aboard the R/V Laurence M. Gould.

方法步驟描述:

  1. From each sampled station one filter was first split in two halves, one for DNA extraction and the other for later RNA studies. 500 µl of the RNAlater from the original tube was loaded onto an Amicon 10 k column and the column was spun for 15 minutes at 14,000 g to get rid of most of the RNAlater and concentrate cells suspended in RNAlater. The resulting solution (~50 µl) was then added back to the one half filter. The cells on filter were lysed by bead-beating using 0.2 g of zirconium beads in 400 µl of buffer AP1 (Qiagen).
  2. DNA was extracted and purified using Qiagen DNeasy Plant Mini kit following the manufacture’s instruction. 18 S (eukaryotic) rDNA gene fragments were amplified by PCR using V4 primer sets: 18 S forward (5′- CCAGCASCYGCGGTAATTCC-3′) and reverse (5′-ACTTTCGTTCTTGAT-3′). Amplicons from each sample were tagged using dual index fusion primers and a “heterogeneity spacer” was used to improve sequencing quality. The “heterogeneity spacer” is a 0–5 bp of spacer added to the index sequence in order to allow different samples be sequenced out of phase and thus improve the amplicon library sequencing quality. Each PCR reaction (25 µl) consisted of 1U of Platinum Taq DNA Polymerase High Fidelity (Invitrogen), 1 × High Fidelity Buffer, 200 µM dNTPs, 2 mM MgSO4, 0.2 µM each primer, and 5–30 ng extracted environmental DNA template. PCR was conducted with an initial activation step at 94 °C for 3 min, followed by 30 three-step cycles consisting of 94 °C for 30 s, 57 °C for 30 s and 72 °C for 1 min, and a final extension step of 72 °C at 10 min. PCR products in triplicates for each sample were then pooled and purified using QIAquick PCR Purification kit, and the concentration of amplicon DNA was quantified using a Qubit dsDNA assay.
  3. Amplicons from different locations were pooled in equimolar amounts (final concentration ~10 ng/µl) and submitted to Duke Institute for Genomic Sciences and Policy (IGSP) for sequencing using Illumina MiSeq. 300PE platform.

引用文獻

  1. Lin, Y., Cassar, N., Marchetti, A., Moreno, C., Ducklow, H., & Li, Z. (2017). Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula. Scientific reports, 7(1), 14845.

額外的詮釋資料

替代的識別碼 fd933a3c-e0a9-4c18-8e95-d1128a2be2ca
https://ipt.biodiversity.aq/resource?r=palmer_lter_eukaryote_18s_plankton