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| griddap | Subset | tabledap | Make A Graph | wms | files | Accessible | Title | Summary | FGDC | ISO 19115 | Info | Background Info | RSS | Institution | Dataset ID | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949101_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_949101_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_949101_v1/ | public | [Eukaryotic viruses encode the ribosomal protein eL40] - NCBI accession metadata for Eukaryotic viruses encoding ribosomal protein eL40 from samples collected on KM1419 and KM1108 from Mar 2011 to Sep 2014 (Giant viruses in the open ocean: Is large size adaptive where cells are scarce?) | This dataset contains sample collection metadata, as well as GenBank accessions and relevant Bioproject numbers for FloV-SA2 samples collected on KM1419 and KM1108 at Station ALOHA from Mar 2011 to Sep 2014.\n\nThis study analyzes the genome of FloV-SA2 (phylum Nucleocytoviricota), a cultured marine virus isolated from open ocean seawater in the Pacific Ocean using a marine microalga strain (UHM3020) in the genus Florenciella (class Dictyochophyceae) as a host. The analysis highlights unique features of the genome, including the encoding of a ribosomal protein (eL40) and a group II viral rhodopsin. The research explores the affiliations and possible origins of these genes, supported by metagenomic and metatranscriptomic data indicating the presence and expression of eL40 in other giant viruses. This study expands the understanding of the metabolic versatility of eukaryoviruses and proposes new mechanisms by which these viruses can manipulate host resources and energy.\n\ncdm_data_type = Other\nVARIABLES:\nTaxa_name (units)\nSource_of_sample (units)\nGenbank_accession (units)\nBioproject_number (units)\nlatitude (degrees_north)\nlongitude (degrees_east)\nDate_Isolated (units)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_949101_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_949101_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_949101_v1/index.htmlTable | https://www.bco-dmo.org/dataset/949101
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_949101_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_949101_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_949101_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_908689_v1/ | public | [Gulf of Alaska copepods: annotated transcriptomes] - Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska) | The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations.\n\nThese data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)\n\ncdm_data_type = Other\nVARIABLES:\nseq_id (unitless)\nGenbank_accession (unitless)\nSpecies (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nDepth_range (meters (m))\nLife_stage (unitless)\nSex (unitless)\nEntry (unitless)\n... (20 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_908689_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_908689_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_908689_v1/index.htmlTable | https://www.bco-dmo.org/dataset/908689
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_908689_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_908689_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_908689_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914459_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914459_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_914459_v1/ | public | [Neocalanus flemingeri incubation experiment: gene expression] - Gene expression profiles for Neocalanus flemingeri pre adults (CV) exposed to four different experimental food conditions collected from the M/V Dora in the Gulf of Alaska at station GAK1 from April 2019 (Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site) | This experimental dataset includes relative expression of individual Neocalanus flemingeri stage CV individuals incubated for different lengths of time and four different food treatments. The experimental protocol and results are described in detail in Roncalli et al., 2023. Briefly, field-collected N. flemingeri were allowed to molt into stage CV and then sorted into four different treatments: no food, low carbon, high carbon and high carbon with diatoms. After a one-week incubation, individuals from all four treatments were processed individually for RNA-Seq. In addition, following two and three-week incubations, copepods from the three fed treatments were processed individually for RNA-Seq. Short-sequence reads were mapped against a reference transcriptome and normalized gene expression was computed for each transcript. The dataset includes log-transformed relative gene expression in reads per kilobase per million reads (RPKM) (log2[RPKM+1]). The dataset also includes a list of differentially expressed genes and a look-up table that cross-references the hierarchical identifications of transcripts generated by the Trinity assembly software and the corresponding National Center for Biotechnology Information (NCBI) accession number. \n\nThese data are further described in the following publications: Roncalli, et al. (2023) (DOI: 10.1093/plankt/fbad045) and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)\n\ncdm_data_type = Other\nVARIABLES:\nseq_id (unitless)\nGenbank_accession (unitless)\nOrganism_Name (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nCollection_date (unitless)\nYear (unitless)\nMonth (unitless)\nDay (unitless)\nDepth_range (meters (m))\n... (33 more variables)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_914459_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_914459_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_914459_v1/index.htmlTable | https://www.bco-dmo.org/dataset/914459
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_914459_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_914459_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_914459_v1 | |||
| https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_931469_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_931469_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_931469_v1/ | public | [Sanger Sequencing Analysis of Potexvirus PCR Products (Potex-5 and Potex-2RC)] - Sanger Sequencing Analysis of Potexvirus PCR Products (Potex-5 and Potex-2RC) collected during West Florida Coastal Surveys of Seagrass from Feb 2022 to Oct 2023 (Collaborative Research: VIDA Seagrass: Viral Infection Dynamics Among Seagrass) | This dataset includes Sanger sequence references for 40 Thalassia testudinum samples collected during systematic seagrass surveys from multiple Florida sites, including Terra Ceia Aquatic Preserve, Tampa Bay seagrass sites S1T5 and S3T8 (Lassing Park), Panacea located in the Florida Panhandle, and Florida Keys sites including Bush Key, Garden Key, Marquesas Key, and Key West.\nWe investigated potexvirus distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed to capture potexvirus diversity in terrestrial plants. The assay, which implements Potex-5 and Potex-2RC primers, successfully amplified a 584 nt RNA-dependent RNA polymerase (RdRp) fragment from TVX-infected seagrasses. Following validation, we screened 74 opportunistically collected, apparently healthy seagrass samples for potexviruses using this RT-PCR assay.\nPotexvirus PCR products were successfully generated from Thalassia testudinum samples. Sequences from these products are deposited in NCBI GenBank under the accession numbers OR827692-OR827705, OR854648, OR863396, OR879052-OR879056, and PP430548-PP430571.\n\ncdm_data_type = Other\nVARIABLES:\nsample (unitless)\nregion (unitless)\nsite (unitless)\ndate (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nsample_host (unitless)\nAphia_id (unitless)\nGenbank_accession (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_931469_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_931469_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_931469_v1/index.htmlTable | https://www.bco-dmo.org/dataset/931469
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_931469_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_931469_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_931469_v1 |