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Southern Ocean Experimental Metatranscriptome to Investigate Micronutrient Colimitation
Citation
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 https://dx.doi.org/10.15468/it9wav

Access data
Archived data
Availability: Creative Commons License This dataset is licensed under a Creative Commons Attribution 4.0 International License.

Description
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. more

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.
Study Extent: 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).
Method step description:
  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.

Scope
Keywords:
Marine, Metadata, Mrna, PSE, Antarctica, Victoria Land, McMurdo Sound, Archaea, Bacteria

Geographical coverage
PSE, Antarctica, Victoria Land, McMurdo Sound [Marine Regions]

Temporal coverage
16 January 2013

Taxonomic coverage
Archaea [WoRMS]
Bacteria [WoRMS]

Parameter
Molecular data

Contributors
Marine Biological Laboratory; The Josephine Bay Paul Center in Camparative Molecular Biology and Evolution, moredata creator
University of Rhode Island, moredata creator
University of Southern California (USC), moredata creator
Virginia Institute of Marine Science (VIMS), moredata creator

Related datasets
Published in:
AntOBIS: Antarctic Ocean Biodiversity Information System, more

Dataset status: Completed
Data type: Metadata
Data origin: Research: field survey
Metadatarecord created: 2019-04-08
Information last updated: 2019-04-10
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