Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments

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

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

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: dbab3d69-c968-4c95-9c6a-b39d02c3c747.  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?:

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

¿Quién puede resolver dudas acerca del recurso?:

Martin Rippin
University of Cologne Cologne DE

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

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

Coordenadas límite Latitud Mínima Longitud Mínima [-62.665, -60.395], Latitud Máxima Longitud Máxima [78.923, 11.925]

Cobertura Taxonómica

microbial meta transcriptome

Dominio  Eukaryote (Eukaryota),  Bacteria (Bacteria),  Archaea (Archaea)

Cobertura Temporal

Fecha Inicial / Fecha Final 2014-08-24 / 2015-02-05

Datos del Proyecto

No hay descripción disponible

Título Polarcrust
Fuentes de Financiación 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).

Personas asociadas al proyecto:

Martin Rippin

Métodos de Muestreo

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

Área de Estudio 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.

Descripción de la metodología paso a paso:

  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).

Referencias 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.

Metadatos Adicionales

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