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99 results for “Tara”
Tara Oceans (2009-2013) rDNA 18S V4 ASV table (DADA2) with nf-core/ampliseq
<p>This repository contains datasets describing the DADA2 ASVs generated from <em>Tara</em> Oceans 18S V4 rDNA data. The ASVs were generated using the nf-core workflow <a href="https://nf-co.re/ampliseq" target="_blank" rel="noopener">ampliseq</a>. Please refer to the readme file (README.html) for more details.</p>
CTD data from leg 5 and thermosalinograph data from legs 5,6,7 of Mission Microbiomes AtlantECO on board SV Tara
<p><strong>Data from the paper "Late summer northwestward Amazon plume pathway under the action of the North Brazil Current rings", Remote Sensing of Environment, Olivier et al., (2024). </strong></p> <p> </p> <p>Thermosalinograph near surface temperature and salinity data from Mission Microbiomes AtlantECO legs 5,6 and 7, from Martinique (France) to Salvador da Bahia (Brazil) in August-September 2021 in a csv or txt format. CTD profiles from the stations effectuated during leg 5 (stations number 35 to 40), in a cnv format. </p> <p>The TSG file is composed of 5 columns: time (Matlab format), longitude (°), latitude (°), SST (°C), SSS (pss).</p> <p>Each CTD file contains one profile, and the corresponding metadata (station number, time, longitude, latitude, units).</p> <p> </p>
Project TARA Survey data
<p>The survey questionnaire and survey response data (anonymized) for Project TARA study on responsible metrics and U.S. academia. </p>
Tara Prokaryote Annotated 16s OTU Counts
<p>"Tara Oceans systematically collected ~35,000 samples for morphological, genetic, and environmental analyses using standardized protocols across multiple depths at global scale, aiming to facilitate a holistic study on how environmental factors and biogeochemical cycles affect oceanic life." (1) "For each prokaryote-enriched sample (N=139), we extracted metagenomic merged Illumina reads (miTAGs) that contained signatures of the 16S rRNA gene (Logares et al. 2013). These fragments were mapped to a set of 16S reference sequences that were downloaded from the SILVA database (Release 115: Quast et al. 2013) and clustered into 97% operational taxonomic units. The OTU count table was summarized at different taxonomic levels." (2)<br> (1): https://www-science-org.offcampus.lib.washington.edu/doi/full/10.1126/science.1261359<br> (2): http://ocean-microbiome.embl.de/companion.html</p>
Green Tara, 14th-15th century CE
Green Tara, 14th-15th century CE, now in the collection of the Minneapolis Institute of Art. From the sculpture's description on [artsmia.org](https://collections.artsmia.org/art/31183/green-tara-tibet) : *Green Tara is one of the most revered female bodhisattvas, a being who postpones enlightenment to assist others on earth. She is the companion of the Cosmic Buddha Amoghasiddhi and equally transmits his gifts to the worshiper. Remarkable for its size and age, this statue is made from pieces of sheet copper—some now missing—that were hammered, formed, and fastened with rivets. The deity's right hand, opened in the gift- bestowing gesture, would have rested on her right knee. Her left hand once held the stem of a lotus, which blossomed at her shoulder.* This model has been repaired for Sketchfab sharing - the upper legs are open in the actual sculpture, but closed and textured in this model. Source: Objaverse 1.0 / Sketchfab
TARA Pacific CDIV cnidarian host taxonomic annotation release version 1_1
<p>This data is the result of the primary analysis of the 18SV9 sequencing data and photos associated with the Coral Diversity dataset collected from all islands as part of the Tara Pacific expedition. A full README is contained within the data upload.</p>
TARA Pacific Bleaching Prevalence of Sampling Sites (Islands)
<p><strong>Summary</strong></p> <p>To obtain a proxy for the stress level of collected corals, we checked for previous occurrences of bleaching events at sampled reef sites by matching island GPS coordinates to the Reef Check dataset (reefcheck.org) obtained from Sully et al (2019). For each Tara Pacific island coordinate, we determined the Reef Check site that was closest (in terms of distance in km); we only considered Reef Check data that was within a 10 km circumference. We further determined short- and long-term climate variables that are known to affect coral stress resilience for all <em>Tara</em> Pacific collection sites that are available from Lombard et al (2022). These data allow to assess if corals from a given site were exposed higher/lower prevalence of thermal stress events and bleaching prior to sampling (over previous years).</p> <p><strong>References</strong></p> <p>Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. <em>Nature Communications</em> <strong>10</strong>, 1264 (2019).</p> <p>Fabien Lombard, Guillaume Bourdin, Stephane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar, Megan Clampitt, Pascal Conan, Ophélie Da Silva, Celine Dimier, Eric Douville, Amanda Elineau, Jonathan Fin, J. Michel Flores, Jean François Ghiglione, Benjamin C.C. Hume, Laetitia Jalabert, Seth G. John, Rachel L. Kelly, Ilan Koren, Yajuan Lin, Dominique Marie, Ryan McMinds, Zoé Mériguet, Nicolas Metzl, David A. Paz-García, Maria Luiza Pedrotti, Julie Poulain, Mireille Pujo-Pay, Josephine Ras, Gilles Reverdin, Sarah Romac, Eric Röttinger, Assaf Vardi, Christian R. Voolstra, Clémentine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Colomban de Vargas, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Emmanuel Boss, Gaby Gorsky. Open science resources from the Tara Pacific expedition across the surface ocean and coral reef ecosystems. <em>Submitted</em> (2022)</p>
Pelagomonas calceolata gene expression in Tara Oceans samples
<p>These files contains the expression levels of all Pelagomonas calceolata nuclear genes (raws) in Tara Oceans samples (columns). Pelago_GeneExpression_TaraOceans_raw_count.tab contains read counts and Pelago_GeneExpression_TaraOceans_TPM.tab contains normalized counts in transcripts per kbp per million (TPM).</p>
rDNA 18S V4 metabarcoding tables (Swarm) for Tara Oceans Expedition (2009-2013), including Tara Polar Circle Expedition (2013)
<p>Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011).<br> Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).</p>
White Tara Mantra
Tara's Mantra wheel in Tibetan. Pronounced Om Tare Tu Tare Tu Tare So Ha. Tara is one of the most beloved figures in Tibetan Buddhism. As a bodhisattva, she helps people pass beyond the troubles of earthly existence and move toward enlightenment. She also protects people from numerous worldly dangers. I create these 3D animated mantras with the intention that this artwork will benefit beings. I create these for free but if you feel inspired to support this work please donate to my Patreon page here: https://www.patreon.com/user?u=32484588&fan_landing=true Source: Objaverse 1.0 / Sketchfab
27 MAGs from the Family of Endozoicomonadaceae derived from Tara Pacific Metagenomes
<p>This dataset contains 27 MAGs from the family of Endozoicomonadaceae generated from a subset of Tara Pacific metagenomes.</p> <p>Contextual information of the MAGs can be found in the associated publication: <strong>Ecology of Endozoicomonadaceae in three coral species across the Pacific Ocean</strong>, Hochart et al, submitted</p> <p> </p>
Tara Nutrient and Flow Cytometry Data
<p>"Tara Oceans systematically collected ~35,000 samples for morphological, genetic, and environmental analyses using standardized protocols across multiple depths at global scale, aiming to facilitate a holistic study on how environmental factors and biogeochemical cycles affect oceanic life. ... Tara Oceans collected seawater samples within the epipelagic layer, both from the surface water and the deep chlorophyll maximum (DCM) layers, as well as the mesopelagic zone." (1)<br> Data provided for time, lat, and lon are mean values based on CTD casts that matched closest in location and depth of the actual sampling locations. This dataset includes environmental, nutrient, diversity, and flow cytometry data associated with samples found in the Tara Eukaryote Annotated 18s OTU Counts and Tara Prokaryote Annotated 16s OTU Counts datasets.</p> <p>(1) https://www-science-org.offcampus.lib.washington.edu/doi/full/10.1126/science.1261359</p>
Tara Eukaryote Annotated 18s OTU Counts
<p>"Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups... Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups."</p> <p>https://www.science.org/doi/10.1126/science.1261605</p>
Data from: The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Open the record for dataset details and reuse information.
RTPR_rnrdb_tara_full-length_amino_acid_sequences
<p>RTPR amino acid sequences used as reference for framshift corrections</p>
FIGURES 26–29 in Cheylostigmaeus tarae sp. nov. and Stigmaeus delaramae sp. nov. (Acari: Stigmaeidae) from Kurdistan, Iran
FIGURES 26–29. Stigmaeus delaramae sp. nov. (Female): 26. Leg I; 27. Leg II; 28. Leg III; 29. Leg IV.
FIGURES 11–16 in Cheylostigmaeus tarae sp. nov. and Stigmaeus delaramae sp. nov. (Acari: Stigmaeidae) from Kurdistan, Iran
FIGURES 11–16. Cheylostigmaeus tarae sp. nov. (Female): 11. Dorsal view; 12. Dorsal setae (vi, ve, sci, c1, d1, d2, f1, h1 & h2); 13. Chelicera; 14. Gnathosoma; 15. Ventral view; 16. Genital region.
FIGURES 21–25 in Cheylostigmaeus tarae sp. nov. and Stigmaeus delaramae sp. nov. (Acari: Stigmaeidae) from Kurdistan, Iran
FIGURES 21–25. Stigmaeus delaramae sp. nov. (Female): 21. Dorsal view; 22. Dorsal setae (vi, ve, c1, c2, d1, f1 & h1); 23. Chelicera; 24. Gnathosoma; 25. Ventral view.
FIGURES 17–20 in Cheylostigmaeus tarae sp. nov. and Stigmaeus delaramae sp. nov. (Acari: Stigmaeidae) from Kurdistan, Iran
FIGURES 17–20. Cheylostigmaeus tarae sp. nov. (Female): 17. Leg I; 18. Leg II; 19. Leg III; 20. Leg IV.
FIGURES 1–6 in Cheylostigmaeus tarae sp. nov. and Stigmaeus delaramae sp. nov. (Acari: Stigmaeidae) from Kurdistan, Iran
FIGURES 1–6. Cheylostigmaeus tarae sp. nov. (Male): 1. Dorsal view; 2. Dorsal setae (vi, ve, c1, c2, d1, f1, h1 & h2); 3. Gnathosoma; 4. Chelicera; 5. Ventral view; 6. Aedeagus.
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OpenNeuro
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