Metadata-only

Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments

Последняя версия опубликована SCAR - Microbial Antarctic Resource System 19 марта 2019 г. SCAR - Microbial Antarctic Resource System
Дата публикации:
19 марта 2019 г.
Лицензия:
CC-BY 4.0

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Описание

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

Версии

В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.

Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: dbab3d69-c968-4c95-9c6a-b39d02c3c747.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:
-

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

Кто может ответить на вопросы о ресурсе:

Martin Rippin
University of Cologne
Cologne
DE

Кем заполнены метаданные:
-

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

Кто еще связан с данным ресурсом:

User

Географический охват

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

Ограничивающие координаты Юг Запад [-62,665, -60,395], Север Восток [78,923, 11,925]

Таксономический охват

microbial meta transcriptome

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

Временной охват

Дата начала / Дата окончания 2014-08-24 / 2015-02-05

Данные проекта

Описание отсутсвует

Название Polarcrust
Финансирование 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).

Исполнители проекта:

Martin Rippin

Методы сбора

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

Охват исследования 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.

Описание этапа методики:

  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).

Библиографические ссылки

  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.

Дополнительные метаданные

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