Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell rDNA SSU V4V5 and 18S V9 metabarcoding from the Tara Oceans expedition (2009-2013)

ABSTRACT: Single cell rDNA 16S V4V5 and 18S V9 metabarcoding from the Tara Oceans expedition (2009-2013)

PROVIDER: PRJEB83903 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

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

Project description: Not available

| S-BSST762 | biostudies-other

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Project description:A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

| S-EPMC5538240 | biostudies-literature

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

Project description:The Holozoa clade comprises animals and several unicellular lineages (choanoflagellates, filastereans, and teretosporeans). Understanding their full diversity is essential to address the origins of animals and other evolutionary questions. However, they are poorly known. To provide more insights into the real diversity of holozoans and check for undiscovered diversity, we here analyzed 18S rDNA metabarcoding data from the global Tara Oceans expedition. To overcome the low phylogenetic information contained in the metabarcoding data set (composed of sequences from the short V9 region of the gene), we used similarity networks by combining two data sets: unknown environmental sequences from Tara Oceans and known reference sequences from GenBank. We then calculated network metrics to compare environmental sequences with reference sequences. These metrics reflected the divergence between both types of sequences and provided an effective way to search for evolutionary relevant diversity, further validated by phylogenetic placements. Our results showed that the percentage of unicellular holozoan diversity remains hidden. We found novelties in several lineages, especially in Acanthoecida choanoflagellates. We also identified a potential new holozoan group that could not be assigned to any of the described extant clades. Data on geographical distribution showed that, although ubiquitous, each unicellular holozoan lineage exhibits a different distribution pattern. We also identified a positive association between new animal hosts and the ichthyosporean symbiont Creolimax fragrantissima, as well as for other holozoans previously reported as free-living. Overall, our analyses provide a fresh perspective into the diversity and ecology of unicellular holozoans, highlighting the amount of undescribed diversity.

| S-EPMC7533066 | biostudies-literature

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.

| PRJEB9738 | ENA

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.

| PRJEB9739 | ENA

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.

| PRJEB9737 | ENA

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.

| PRJEB9691 | ENA

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.

| PRJEB9741 | ENA

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

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

| PRJEB9740 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data