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BNA. Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for small DNA viruses.

ABSTRACT: Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for small DNA viruses.

PROVIDER: PRJEB9742 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2762100_1.fastq.gz	Fastqsanger.gz
	ERR2762100_2.fastq.gz	Fastqsanger.gz
	ERR2762110_1.fastq.gz	Fastqsanger.gz
	ERR2762110_2.fastq.gz	Fastqsanger.gz
	ERR2762120_1.fastq.gz	Fastqsanger.gz

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BHN - Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

Project description:Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

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BHQ. Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

Project description:Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

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BII. Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

Project description:Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

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BIK. Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

Project description:Metatranscriptome sequencing from Tara Oceans Polar Circle samples corresponding to size fractions for protists.

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BMR. Metatranscriptome sequencing from Tara Oceans Polar Circle RNA samples corresponding to size fractions for prokaryotes.

Project description:Metatranscriptome sequencing from Tara Oceans Polar Circle RNA samples corresponding to size fractions for prokaryotes.

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BMI. Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for prokaryotes.

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18S rDNA miTags information for Tara Oceans Expedition (2009-2013), including the Tara Polar Circle Expedition (2013)

Project description: Not available

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TARA Oceans Viral Proteins - Illuminating structural proteins in viral "dark matter" with metaproteomics

Project description:A grand challenge in biology is the lack of annotation for much of global sequence space. In particular, while microbes and their viruses are critical to Earth System functioning, surveys of their communities in nature routinely return genes of unknown function, particularly for viruses. This hampers understanding and predictive capability, and reflects a number of database limitations. Here we apply high-resolution environmental metaproteomics to 4 purified viral concentrates from the Tara Oceans Expedition to identify in situ proteins extracted from uncultivated viral particles. Using matched metagenomic databases, we identified 1875 proteins belonging to 549 non-redundant protein clusters that are predominantly of unknown function. These data help identify function for structure-associated proteins in known abundant tailed viruses (e.g., pelagiphages and cyanophages) and validate newly-identified uncultured viral sequences linked to abundant novel hosts. One protein cluster alone comprised 22% of the identified structure-associated proteins, with ~46% of the observed spectra. Structural modeling of this highly abundant viral protein cluster indicates its likely role as a novel, previously unknown capsid. Together these analyses provide much-needed, culture-independent structure-associated protein annotations critical for identifying viral signals across diverse datasets to better elucidate viral roles in nature.

2016-02-25 | PXD000938 | Pride

DNA Microarray of B16F10 cells treated with or without 25 micromolar of tara tannin

Project description:The experiment was designed to determine the global gene expression changes in B16F10 cells as a result of treatment with 25 micromolar of tara tannin

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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.

Project description:Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6??m size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10(4)-10(5) genomes?ml(-1) for the samples from the photic zone and 10(2)-10(3) genomes?ml(-1) for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.

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