Palmer LTER 2014 cruise microbial Eukaryote (18s) plankton

最新バージョン SCAR - Microbial Antarctic Resource System により出版 3月 19, 2019 SCAR - Microbial Antarctic Resource System
公開日:
2019年3月19日
ライセンス:
CC-BY 4.0

メタデータのみリソース のメタデータの最新版をEML または RTF としてダウンロード:

EML ファイルとしてのメタデータ ダウンロード English で (10 KB)
RTF ファイルとしてのメタデータ ダウンロード English で (12 KB)

説明

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.

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

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

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: fd933a3c-e0a9-4c18-8e95-d1128a2be2caが割り当てられています。   Scientific Committee on Antarctic Research によって承認されたデータ パブリッシャーとして GBIF に登録されているSCAR - Microbial Antarctic Resource System が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

Yajuan Lin
  • 最初のデータ採集者
  • 連絡先
Duke University
Durham
US
Nicolas Cassar
  • 最初のデータ採集者
Duke University
Durham
US
Adrian Marchetti
  • 最初のデータ採集者
University of North Carolina at Chapel Hill
Chapel Hill
US
Carly Moreno
  • 最初のデータ採集者
University of North Carolina at Chapel Hill
Chapel Hill
US
Hugh Ducklow
  • 最初のデータ採集者
Columbia University
Palisades
US
Zuchuan Li
  • 最初のデータ採集者
Duke University
Durham
US
Maxime Sweetlove
  • メタデータ提供者
Research assistent
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
BE

地理的範囲

Southern Ocean around the Western Antarctic Peninsula.

座標(緯度経度) 南 西 [-68.287, -74.184], 北 東 [-63.965, -63.403]

生物分類学的範囲

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

Domain Eukaryota (Eukaryotes)

プロジェクトデータ

説明がありません

タイトル LTER_2014
ファンデイング 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”.

プロジェクトに携わる要員:

Yajuan Li
Nicolas Cassar

収集方法

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.

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

Method step description:

  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.

書誌情報の引用

  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.

追加のメタデータ

代替識別子 fd933a3c-e0a9-4c18-8e95-d1128a2be2ca
https://ipt.biodiversity.aq/resource?r=palmer_lter_eukaryote_18s_plankton