Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments

Somente metadatos
Versão mais recente published by SCAR - Microbial Antarctic Resource System on mar 19, 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de março de 2019
Licença:
CC-BY 4.0

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Descrição

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

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: dbab3d69-c968-4c95-9c6a-b39d02c3c747.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

Palavras-chave

Metadata

Contatos

Martin Rippin
  • Originador ●
  • Ponto De Contato
University of Cologne
Cologne
DE
Laura Williams
  • Originador
University of Kaiserslautern
Kaiserslautern
DE
Claudia Colesie
  • Originador
Swedish University of Agricultural Sciences
Umea
SE
Nadine Borchardt
  • Originador
University of Rostock
Rostock
DE
Patrick Jung
  • Originador
University of Kaiserslautern
Kaiserslautern
DE
Burkhard Budel
  • Originador
University of Kaiserslautern
Kaiserslautern
DE
Ulf Karsten
  • Originador
University of Rostock
Rostoc
DE
Burkhard Becker
  • Originador
University of Cologne
Cologne
DE
Maxime Sweetlove
  • Provedor Dos Metadados
  • Research assistent
Royal Belgian Institute of Natural Sciences
  • Rue Vautier 29
1000 Brussels
BE

Cobertura Geográfica

Livinston Island, near the Juan Carlos I base (Antarctica); and Ny-Alsesund on Svalbard (Arctic)

Coordenadas delimitadoras Sul Oeste [-62,665, -60,395], Norte Leste [78,923, 11,925]

Cobertura Taxonômica

microbial meta transcriptome

Domínio Eukaryote (Eukaryota), Bacteria (Bacteria), Archaea (Archaea)

Cobertura Temporal

Data Inicial / Data final 2014-08-24 / 2015-02-05

Dados Sobre o Projeto

Nenhuma descrição disponível

Título Polarcrust
Financiamento This study was funded by the Deutsche Forschungsgemeinschaft (DFG) within the project ‘Polarcrust’ (BE1779/18-1, KA899/23-1, BU666/17-1) which is part of the Priority Program 1158 ‘Antarctic Research’. Sampling and research activities were approved by the German authorities (Umwelt Bundesamt: Biological soil crust algae from the polar regions; 24.09.2014).

O pessoal envolvido no projeto:

Martin Rippin

Métodos de Amostragem

Samples (1 g) were taken aseptically, and were preserved using the LifeGuard™ Soil Preservation Solution (MO BIO Laboratories, Carlsbad, CA, USA).

Área de Estudo 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.

Descrição dos passos do método:

  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).

Citações bibliográficas

  1. Rippin, M., Borchhardt, N., Williams, L., Colesie, C., Jung, P., Büdel, B., ... & Becker, B. (2018). Genus richness of microalgae and Cyanobacteria in biological soil crusts from Svalbard and Livingston Island: morphological versus molecular approaches. Polar Biology, 41(5), 909-923. https://doi.org/10.1007/s00300-018-2252-2
  2. Williams, L., Borchhardt, N., Colesie, C., Baum, C., Komsic-Buchmann, K., Rippin, M., ... & Büdel, B. (2017). Biological soil crusts of Arctic Svalbard and of Livingston Island, Antarctica. Polar Biology, 40(2), 399-411.

Metadados Adicionais

Identificadores alternativos dbab3d69-c968-4c95-9c6a-b39d02c3c747
https://ipt.biodiversity.aq/resource?r=polar_microbial_mat_metatranscriptome