Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 2019 SCAR - Microbial Antarctic Resource System

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

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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : dbab3d69-c968-4c95-9c6a-b39d02c3c747.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:

Martin Rippin
University of Cologne Cologne DE
Laura Williams
University of Kaiserslautern Kaiserslautern DE
Claudia Colesie
Swedish University of Agricultural Sciences Umea SE
Nadine Borchardt
University of Rostock Rostock DE
Patrick Jung
University of Kaiserslautern Kaiserslautern DE
Burkhard Budel
University of Kaiserslautern Kaiserslautern DE
Ulf Karsten
University of Rostock Rostoc DE
Burkhard Becker
University of Cologne Cologne DE

Personne pouvant répondre aux questions sur la ressource:

Martin Rippin
University of Cologne Cologne DE

Personne ayant renseigné les métadonnées:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

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

Enveloppe géographique Sud Ouest [-62.665, -60.395], Nord Est [78.923, 11.925]

Couverture taxonomique

microbial meta transcriptome

Domain  Eukaryote (Eukaryota),  Bacteria (Bacteria),  Archaea (Archaea)

Couverture temporelle

Date de début / Date de fin 2014-08-24 / 2015-02-05

Données sur le projet

Pas de description disponible

Titre Polarcrust
Financement 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).

Les personnes impliquées dans le projet:

Martin Rippin

Méthodes d'échantillonnage

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

Etendue de l'étude 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.

Description des étapes de la méthode:

  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).

Citations bibliographiques

  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.

Métadonnées additionnelles

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