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99 results for “Tara”
UCSF TARA Study: Training for Awareness, Resilience and Action
ClinicalTrials.gov study NCT02480257. IPD Sharing: Not stated. Countries: 1. Publications: 0.
TARA for Medical Students, a Single-arm Mixed Methods Pilot Study
ClinicalTrials.gov study NCT05059392. IPD Sharing: NO. Countries: 1. Publications: 0.
Safety and Toxicity Study of Intravesical Instillation of TARA-002 in Adults with High-grade Non-muscle Invasive Bladder Cancer (Phase 1b)
ClinicalTrials.gov study NCT05085990. IPD Sharing: NO. Countries: 1. Publications: 0.
Tara microbiome
Tara microbiome is the latest Tara expedition focused on plankton. The Microbiome Mission will help us understand the services provided by this essential ecosystem of the Ocean, its microbiome, an increasingly crucial challenge for scientific research and is done in conjunction with the AtlantECO program where additional ships will collect similar variables.
TARA-EUROPA
For two consecutive years (2023-2024), the schooner Tara is participating in the study of coastal ecosystems all along the European coast. The sampling of Tara Europa is part of the TREC expedition Traversing European Coastlines, led by the European Molecular Biology Laboratory (EMBL) in collaboration with the Tara OceanS consortium, the Tara Ocean Foundation and more than 70 scientific institutions. Its objective is to study the land-sea interface, where biodiversity meets numerous pollutions.
Tara Mediterranean Expedition in 2014
Over the past decades, the proliferation of plastics has rapidly become a global problem affecting all oceans. With 80% of plastics in the sea originating from land, this pollution highlights the interactions between our daily lives and the ocean, and reinforces the need for a transition to an economy that is more respectful of the planet. During the Tara Mediterranean expedition in 2014, the schooner crisscrossed the Mare nostrum to study the interaction of plastics with plankton, and biodiversity in general. First edifying observation: of the 2000 samples taken during the expedition from 350 different sites, all contained plastic fragments.
Tara Oceans Expedition
The Tara Oceans expedition, a 2.5-year long and 57,000 mile long trajectory, was conceived to provide a snapshot of the distribution of planktonic organisms in the world ocean, providing 'A global-scale study of morphological, genetic, and functional biodiversity of plankton organisms in relation to the changing physico-chemical parameters of the oceans' (Karsenti et al., 2011). The expedition took place from September 2009 to March 2012, spanned the majority of the world's oceans, and included, besides a large array of biological sampling, hydrographic measurements, optical measurements of surface hyper-spectral particulate absorption and attenuation, hyper-spectral reflectance and HPLC pigments.E. Karsenti, S.G. Acinas, P. Bork, C. Bowler, C. De Vargas, J. Raes, and 22 co-authors, A holistic approach to marine eco-systems biology, PLoS Biol. 9, e1001177, (2011), doi:10.1371/journal.pbio.1001177.
FIGURE 1 in Aegiochus gracilipes (Hansen, 1895) a senior synonym of Aegiochus tara Bruce 2009 (Crustacea: Isopoda: Aegidae)
FIGURE 1. Aegiochus gracilipes (Hansen, 1895), female 27.0 mm, NHM UK 2018.1255, North Eastern Atlantic Ocean (Porcupine Seabight & Porcupine Abyssal Plain). Scale marks 1 mm.
TARA Working Prototype [Version 2]: Feasibility Study
ClinicalTrials.gov study NCT04320524. IPD Sharing: NO. Countries: 0. Publications: 0.
Tara Oceans Pacific Expedition
Data measured during the Tara Oceans Pacific Expedition, 2016-2018
Tara Oceans Polar Circle 2013 Expedition
Tara Oceans Polar Circle 2013
RNA-seq analysis of mouse NSCLC tissues in the PBS, Taraxasterol (Tara), DC tumor vaccine and Taraxasterol combined with DC tumor vaccine group
GEO Series GSE245586. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1
<p>The tables in this dataset associate metabarcoding sequencing files generated by Genoscope (i.e. fastq.gz files with informative filename structures; with sequencing file pairs associated to unique 'readset' identifiers; housed on their FTP server at www.genoscope.cns.fr/sadc/tarapacific/METABARCODING; with the 'METAB' sequence strategy identifier as part of the sequencing file name) with their associated 'sample-id_source' identifier; as detailed in the 'TARA-PACIFIC_samples-provenance' file part of the 'Tara Pacific samples provenance and environmental context' Zenodo publication (DOI: 10.5281/zenodo.4068292) part of the 'tarapacific' Zenodo community). The main purpose of these tables is to act as a reference to identify samples (i.e., with a single 'sample-id_source') for which sequencing replication exists, per primer set (i.e., more than one set of fastq.gz sequencing files were generated, pre primer set). In the case of replication, these tables classify the replication into three classes color coded as green (same DNA extraction, same PCR, same sequencing run, different sequencing lane), yellow (same DNA extraction, same PCR, different sequencing run) and red (different DNA extraction and/or different PCR). It should be noted that in the vast majority of cases a 'sample-id_source' associates to only one readset per primer set. For a full description of the dataset, please see the included README.</p>
Tara Pacific 16S rRNA data analysis release
<p>This data is the result of the primary analysis of the 16S rRNA gene sequencing data collected from all islands as part of the Tara Pacific expedition. The analysis was conducted using cutadapt/snakemake/dada2 and usearch. A full README is contained within the data upload.</p> <p> </p> <p><strong>Taxonomic abundance tables (ASVs, OTUs) released together with the TARA Pacific <a href="https://www.nature.com/collections/adgaiffggg">publications</a></strong><strong> can be found in <a href="https://zenodo.org/record/4451892">Version 1.1.0</a> of this repository. </strong></p>
04082023_Tara_Neg
<p>DDA analysis in negative mode of environmental samples from Tara TREC campaign.</p>
03082023_Tara_Pos
<p>DDA in positive mode of environmental samles from the TREC campaign.</p>
rDNA 18S V9 ASV tables (SWARM) for Tara Pacific Expedition
<p>This data is the result of the second analysis of the V9 18S rDNA metabarcoding sequencing data from the <em>Tara</em> Pacific expedition. The analysis was conducted using cutadapt, vsearch, swarm and lulu. Please refer to the readme file for more details.</p>
Single cell rDNA 16S V4V5 and 18S V9 metabarcoding tables (dada2) from the Tara Oceans expedition (2009-2013)
<p>Single cell rDNA 16S V4V5 and 18S V9 metabarcoding tables (dada2) from the Tara Oceans expedition (2009-2013). The code to generate the ASV tables is here: https://gitlab.com/tara-and-friends-euk-metab/tara-single-cell-metab</p>
Tara Oceans (2009-2013) rDNA 16S V4V5 ASV table (dada2)
<p>This repository contains a rDNA 16S V4V5 ASV table (TARA-Oceans_16S-V4V5_dada2_table.tsv.gz) for <em>Tara</em> Oceans (2009-2013).</p> <p>In the file <strong>TARA-Oceans_16S-V4V5_dada2_table.tsv.gz</strong>, each ASV, one per row, is described by the following fields: <strong>amplicon</strong> = ASV identifier; <strong>taxonomy</strong> = taxonomic path assigned to the ASV using IDTAXA; <strong>confidence</strong> = IDTAXA confidence scores for each taxonomic rank; <strong>total</strong> = total number of reads for the entire dataset; <strong>spread</strong> = number of samples in which the ASV is detected; <strong>sequence</strong> = ASV nucleic acid sequence; <strong>TARA_XXXXXXXXXX</strong> = number of reads in each of the 1,134 <em>Tara</em> Oceans samples.</p> <p>Detailed information about DNA extraction, PCR amplification and Illumina sequencing of metabarcodes, as well as subsequent sequence data cleaning and taxonomic assignment can be found in (Alberti et al. 2017). Briefly, DNA samples were amplified by PCR targeting the hypervariable region V4V5 (primer pair: 15F-Y 5′- GTGYCAGCMGCCGCGGTAA-3′ and 926R 5′- CCGYCAATTYMTTTRAGTTT-3′ 16S primers; (Parada et al. 2016)) of the 16S rRNA marker gene followed by the high-throughput sequencing of the amplicons. The details of PCR mixes, thermocycling and sequencing conditions are provided in Alberti et al. (2017).</p> <p>Resulting paired-end reads were mixed-oriented meaning that both R1 and R2 files are composed by a mix of forward and reverse reads. Paired-end reads were trimmed to remove PCR primer sequences using Cutadapt v2.7 (Martin, 2011) and dispatched into four files, 2 files for the classical orientation (forward reads in R1 and reverse reads in R2) and 2 others for the other orientation (reverse reads in R1 and forward reads in R2). Paired-end reads without both primers were filtered out using the option --discard-untrimmed. Forward and reverse reads were trimmed at position 215 and 190 for R1 and R2 files respectively. Reads with ambiguous nucleotides or with a maximum number of expected errors (maxEE) superior to 2 were filtered out using the function filterAndTrim() from the R package dada2 (Callahan et al., 2016). For each run and read orientation, error rates were defined using the function learnErrors() and denoised using the dada() function with pool = TRUE before being merged using mergePairs() with default parameters. Mixed orientated reads from the same sample and sequencing replicates were summed together. Remaining chimeras were removed using the function removeBimeraDenovo(). Scripts producing the ASV table are publicly available here: https://gitlab.univ-nantes.fr/combi-ls2n/taradada.</p> <p>ASVs were taxonomically assigned using IDTAXA (50% confidence threshold) (Murali, Bhargava, and Wright 2018) with SILVA v138.</p> <p>Alberti, A., Poulain, J., Engelen, S., Labadie, K., Romac, S., Ferrera, I., Albini, G., Aury, J.-M., Belser, C., Bertrand, A., Cruaud, C., Da Silva, C., Dossat, C., Gavory, F., Gas, S., Guy, J., Haquelle, M., Jacoby, E., Jaillon, O., Lemainque, A., Pelletier, E., Samson, G., Wessner, M., Genoscope Technical Team, Bazire, P., Beluche, O., Bertrand, L., Besnard-Gonnet, M., Bordelais, I., Boutard, M., Dubois, M., Dumont, C., Ettedgui, E., Fernandez, P., Garcia, E., Aiach, N.G., Guerin, T., Hamon, C., Brun, E., Lebled, S., Lenoble, P., Louesse, C., Mahieu, E., Mairey, B., Martins, N., Megret, C., Milani, C., Muanga, J., Orvain, C., Payen, E., Perroud, P., Petit, E., Robert, D., Ronsin, M., Vacherie, B., Acinas, S.G., Royo-Llonch, M., Cornejo-Castillo, F.M., Logares, R., Fernández-Gómez, B., Bowler, C., Cochrane, G., Amid, C., Hoopen, P.T., De Vargas, C., Grimsley, N., Desgranges, E., Kandels-Lewis, S., Ogata, H., Poulton, N., Sieracki, M.E., Stepanauskas, R., Sullivan, M.B., Brum, J.R., Duhaime, M.B., Poulos, B.T., Hurwitz, B.L., Tara Oceans Consortium Coordinators, Acinas, S.G., Bork, P., Boss, E., Bowler, C., De Vargas, C., Follows, M., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Kandels-Lewis, S., Karp-Boss, L., Karsenti, E., Not, F., Ogata, H., Pesant, S., Raes, J., Sardet, C., Sieracki, M.E., Speich, S., Stemmann, L., Sullivan, M.B., Sunagawa, S., Wincker, P., Pesant, S., Karsenti, E., Wincker, P., 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 4, 170093. <a href="https://doi.org/10.1038/sdata.2017.93">https://doi.org/10.1038/sdata.2017.93</a></p> <p>Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., Holmes, S.P., 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583. <a href="https://doi.org/10.1038/nmeth.3869">https://doi.org/10.1038/nmeth.3869</a></p> <p>Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet j. 17, 10. <a href="https://doi.org/10.14806/ej.17.1.200">https://doi.org/10.14806/ej.17.1.200</a></p> <p>Murali, A., Bhargava, A., Wright, E.S., 2018. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6, 140. <a href="https://doi.org/10.1186/s40168-018-0521-5">https://doi.org/10.1186/s40168-018-0521-5</a></p>
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.