Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 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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Versiones

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: ddd527ae-1539-4189-ac4a-a731640badcf.  SCAR - Microbial Antarctic Resource System publica este recurso, y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras Clave

Metadata

Contactos

¿Quién creó el recurso?:

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

¿Quién puede resolver dudas acerca del recurso?:

Erin Bertrand
J. Craig Venter Institute La Jolla US

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

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

Coordenadas límite Latitud Mínima Longitud Mínima [-77.617, 164.474], Latitud Máxima Longitud Máxima [-77.617, 164.474]

Cobertura Taxonómica

RNA metatranscriptome

Dominio  Eukaryota (Eukaryotes),  Bacteria (Bacteria),  Archaea (Archaea)

Cobertura Temporal

Fecha Inicial 2013-01-16

Datos del Proyecto

No hay descripción disponible

Título Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation
Fuentes de Financiación 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.

Personas asociadas al proyecto:

Erin Bertrand
Andrew Allen
Deborah Bronk
David Hutchins
Anton Post

Métodos de Muestreo

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.

Área de Estudio 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).

Descripción de la metodología paso a paso:

  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.

Referencias Bibliográficas

  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.

Metadatos Adicionales

Identificadores Alternativos ddd527ae-1539-4189-ac4a-a731640badcf
https://ipt.biodiversity.aq/resource?r=southern_ocean_experimental_metatranscriptome