Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation

最新版本 由 SCAR - Microbial Antarctic Resource System 發佈於 Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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.

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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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The publisher and rights holder of this work is 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

資源建立者:

Erin Bertrand
J. Craig Venter Institute La Jolla US
John McCrow
J. Craig Venter Institute La Jolla US
Ahmed Moustafa
J. Craig Venter Institute La Jolla US
Hong Zheng
J. Craig Venter Institute La Jolla US
Jeffrey McQuaid
J. Craig Venter Institute La Jolla US
Tom Delmont
josephine Bay Paul Center Woods Hole US
Anton Post
University of Rhode Island Narragansett US
Rachel Sipler
Virginia Institute of Marine Science Gloucester Point US
Jenna Spackeen
Virginia Institute of Marine Science Gloucester Point US
Kai Xu
University of Southern California Los Angeles US
Deborah Bronk
Virginia Institute of Marine Science Gloucester Point US
David Hutchins
Professor
University of Southern California Los Angeles US
Andrew Allen
J. Craig Venter Institute La Jolla US

可回覆此資源相關問題者:

Erin Bertrand
J. Craig Venter Institute La Jolla US

元數據填寫者:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 Brussels BE

與此資源的相關者:

使用者

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.

The personnel involved in the project:

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.

額外的元數據

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