Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation

最新版本 published by SCAR - Microbial Antarctic Resource System on 3月 19, 2019 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
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CC-BY 4.0

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說明

Metatranscriptome dataset (targeting all mRNA) from Southern Ocean sea water samples (1 control, 3 treatments, 3 replicates per treatment), near the ice edge at McMurdo Sound (Antarctica). All samples were incubated 24h at 0°C, ~45 μmol photons m-2 s-1 of constant light. Treatments existed of: 1) addition of 1 nM FeCl3; 2) addition of 200 pM cyanocobalamin; or 3) addition of 200 pM cyanocobalamin and 1 nM FeCl3.

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。:

Bertrand E, McCrow J, Moustafa A, Zheng H, McQuaid J, Delmont T, Post A, Sipler R, Spackeen J, Xu K, Bronk D, Hutchins D, Allen A (2019): Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome&v=1.2

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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: ddd527ae-1539-4189-ac4a-a731640badcf。  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

Erin Bertrand
  • 出處
  • 連絡人
J. Craig Venter Institute
La Jolla
US
John McCrow
  • 出處
J. Craig Venter Institute
La Jolla
US
Ahmed Moustafa
  • 出處
J. Craig Venter Institute
La Jolla
US
Hong Zheng
  • 出處
J. Craig Venter Institute
La Jolla
US
Jeffrey McQuaid
  • 出處
J. Craig Venter Institute
La Jolla
US
Tom Delmont
  • 出處
josephine Bay Paul Center
Woods Hole
US
Anton Post
  • 出處
University of Rhode Island
Narragansett
US
Rachel Sipler
  • 出處
Virginia Institute of Marine Science
Gloucester Point
US
Jenna Spackeen
  • 出處
Virginia Institute of Marine Science
Gloucester Point
US
Kai Xu
  • 出處
University of Southern California
Los Angeles
US
Deborah Bronk
  • 出處
Virginia Institute of Marine Science
Gloucester Point
US
David Hutchins
  • 出處
  • Professor
University of Southern California
Los Angeles
US
Andrew Allen
  • 出處
J. Craig Venter Institute
La Jolla
US
Maxime Sweetlove
  • 元數據提供者
  • Research assistent
Royal Belgian Institute for Natural Sciences
  • Rue Vautier 29
Brussels
BE

地理涵蓋範圍

Souther Ocean sea water of the ice edge, near McMurdo Sound, Antarctica

界定座標範圍 緯度南界 經度西界 [-77.617, 164.474], 緯度北界 經度東界 [-77.617, 164.474]

分類群涵蓋範圍

RNA metatranscriptome

Domain Eukaryota (Eukaryotes), Bacteria (Bacteria), Archaea (Archaea)

時間涵蓋範圍

起始日期 2013-01-16

計畫資料

無相關描述

計畫名稱 Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation
經費來源 This study was funded by National Science Foundation (NSF) Antarctic Sciences Awards 1103503, 0732822 and 1043671, 1043748, 1043635, and 1142095; Gordon and Betty Moore Foundation Grant GBMF3828; and NSF Ocean Sciences Award 1136477.

參與計畫的人員:

Erin Bertrand
Andrew Allen
Deborah Bronk
David Hutchins
Anton Post

取樣方法

Water was pumped to the surface using a trace metal clean diaphragm pump and acid cleaned teflon tubing and dispensed into trace metal clean (TMC) 50 L carboys. Sampling occurred between 18:00 and 19:00 in open air, with wind coming from over open water, NNE to NE. The carboys were protected from light with dark plastic bags and returned to the Crary Laboratory at McMurdo Station via helicopter within one hour of sampling, where it was stored overnight at 0°C and then split into twelve 2.7 L TMC polycarbonate bottles.

研究範圍 On 16 Jan 2013, seawater was collected from 3 m depth at the sea ice edge in McMurdo Sound of the Ross Sea (77° 36.999’ S 165° 28.464’ E).

方法步驟描述:

  1. Three bottles were left as unamended controls, three were amended with 1 nM FeCl3, three were amended with 200 pM cyanocobalamin, and three had 200 pM cyanocobalamin and 1 nM Fe added. Iron concentrations in the cobalamin stock were such that < 6 pM iron was added with 200 pM cobalamin (measured via flow injection). Bottles were placed in an indoor incubator at 0°C, ~45 μmol photons m-2 s-1 of constant light. This level of irradiance is in between levels typical for 3 m depth in open water and under the sea ice, and was selected because the harvested community would have experienced both under ice and open water light regimes in the recent past.
  2. For RNA extraction, 1 billion copies of each of two RNA standards were added to each filter (#1, #8 ArrayControl Spots and Spikes, Life Technologies, with polyA tails). RNA was extracted from Sterivex filters using the Trizol reagent manufacturer’s protocol (Life Technologies); Trizol was added to the filter membrane after it had been extracted from the plastic housing on dry ice using a sterile pipe cutter, razor blade, and forceps. 450- 800 ng RNA was obtained per filter. RNAeasy MinElut Cleanup kit was applied (Qiagen) and ribosomal RNA was removed with Ribo-Zero Magnetic kits, employing a mix of plant, bacterial, and human/mouse/rat formulations in a ratio of 2:1:1 (Epicentre).
  3. The resulting mRNA enrichment was purified using an Agencourt RNAClean XP kit and 2 ng of rRNA depleted RNA was subjected to amplification and cDNA synthesis using the Ovation RNA-Seq System V2 (NuGEN), which applies both polyA and random hexamer primers. 1 μg of the resulting high quality cDNA pool was fragmented to a mean length of 200 bp. Libraries were constructed using a Truseq RNA Sample Prep kit v2 (IlluminaTM), applying the manufacturer’s protocol from the end-repair step. The libraries were then subjected to paired-end sequencing via Illumina Hiseq.

引用文獻

  1. Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., ... & Bronk, D. A. (2015). Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proceedings of the National Academy of Sciences, 112(32), 9938-9943.

額外的詮釋資料

替代的識別碼 ddd527ae-1539-4189-ac4a-a731640badcf
https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome