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Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments
Citation
Rippin M, Williams L, Colesie C, Borchardt N, Jung P, Budel B, Karsten U, Becker B (2019): Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=polar_microbial_mat_metatranscriptome&v=1.1 https://dx.doi.org/10.15468/e2zhxj

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

Description
Metatranscriptome dataset (Illumina HiSeq) of RNA from soil microbial mat samples in Arctic (Svalbard) and Antarctic (Livingston Island) polar tundra environments. more

Samples (1 g) were taken aseptically, and were preserved using the LifeGuard™ Soil Preservation Solution (MO BIO Laboratories, Carlsbad, CA, USA).
Study Extent: Soil crust samples were collected during expeditions to the Arctic and Antarctica in August 2014 and February 2015, respectively. Arctic samples were taken near the station Ny-Ålesund. The Antarctic samples were collected close by the Spanish Juan Carlos I Antarctic Base at Livingston Island, South Shetland Islands.
Method step description:
  1. The Arctic samples (NA) were processed according to Rippin et al. (2016) using the CTAB protocol, DNase I (Thermo Fisher Scientific, Waltham, MA, USA) and the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Due to low RNA yields, a total of six biological replicates were extracted and combined to obtain three pooled replicates. RNA from three biological replicates, collected at Livingston Island (Gr1), was isolated using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA), treated with DNase I (Thermo Fisher Scientific, Waltham, MA, USA) and purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) as described by Rippin et al. (2016). Single samples yielded sufficient amounts of RNA.
  2. All RNA samples were further processed by Eurofins Genomics (Ebersberg, Germany). The processing included quality control utilizing the BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and library preparation for both triplicates. Eukaryotic mRNA was enriched using oligo-(dT) beads, fragmented and, subsequently, cDNA was synthesized using random hexamers. Finally, Illumina compatible adapters were ligated. The libraries of the individual samples NÅ and Gr1 were applied to an Illumina HiSeq 2500, all triplicates multiplexed on one lane, using 125 bp paired-end and single-end mode, respectively. For sample NÅ, the HiSeq Control Software 2.2.58, RTA 1.18.64 and bcl2fastq-1.8.4 were used while the detected signals from sample Gr1 were processed by operating the HiSeq Control Software 2.2.38, RTA 1.18.61 and bcl2fastq-1.8.4 (Illumina, San Diego, CA, USA).

Scope
Keywords:
Terrestrial, Metadata, Microbial mats, RNA, Tundra soils, ANE, Norway, Svalbard, Antarctica, Archaea, Bacteria

Geographical coverage
ANE, Norway, Svalbard Stations [Marine Regions]
Ny-Alsesund
Antarctica Stations [Marine Regions]
Livinston Island, near the Juan Carlos I base

Temporal coverage
24 August 2014 - 5 February 2015

Taxonomic coverage
Archaea [WoRMS]
Bacteria [WoRMS]

Parameter
Molecular data

Contributors
Swedish University of Agricultural Sciences (SLU), moredata creator
Technical University of Kaiserslautern (TUK), moredata creator
Universität Rostock, moredata creator
University of Cologne, 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: 2019-04-03
Information last updated: 2019-04-10
All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy