BCO-DMO ERDDAP
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https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_675040 https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_675040/ public Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) This dataset reports Salpa thompsoni specimens used for\ngenomics/transcriptomics with their GenBank accession links.\n \nRelated Dataset: [Salp sample log](\\\\https://www.bco-\ndmo.org/dataset/672600\\\\)\n\ncdm_data_type = Other\nVARIABLES:\nspecimen (unitless)\ncruise_id (unitless)\nstation (unitless)\nlength (millimeters)\nSRA_accession (unitless)\nBioSample_accession (Bio Sample Accession, unitless)\nSRA_accession_link (unitless)\nBioSample_accession_link (Bio Sample Accession Link, unitless)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_675040_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_675040/index.htmlTable https://www.bco-dmo.org/dataset/675040 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_675040.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_675040&showErrors=false&email= BCO-DMO bcodmo_dataset_675040
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817298 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817298.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_817298/ public Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB coral gene expression at two time points: September 2017, when surface water salinity was reduced (\\u223c34 ppt); and 1 month later when salinity had returned to typical levels (\\u223c36 ppt in October 2017). \\r\\n\\r\\nThis dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information.  It also contains sample information and species names for samples collected the east and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) at 80ft.\\r\\n\\r\\nThese data were published in Wright et al. (2019).\n\ncdm_data_type = Other\nVARIABLES:\nSample_Name (unitless)\ntime2 (Time, unitless)\nBank (unitless)\nBuoy (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nSpecies (unitless)\ndepth (m)\nSRA (unitless)\nAccession (unitless)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_817298_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_817298/index.htmlTable https://www.bco-dmo.org/dataset/817298 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_817298.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_817298&showErrors=false&email= BCO-DMO bcodmo_dataset_817298
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_768550.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_768550 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_768550.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_768550/ public DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013 Metadata for assembled contigs and ORFS from metatranscriptome analysis from CTD casts in the Monterey Bay area on RV/Point Sur cruise PS1312, June-July 2013. Assembled contigs files are also available; see Supplemental Files.\n\ncdm_data_type = Other\nVARIABLES:\nBioProject_type (Bio Project Type, unitless)\nBioProject_id (Bio Project Id, unitless)\nBioSample (Bio Sample, unitless)\nSample_name (unitless)\nSRA_id (unitless)\nPackage_type (unitless)\nversion (unitless)\nAccession (unitless)\nID (unitless)\ncruise_id (unitless)\nCTD_cast (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\nDate_collection (unitless)\nstation (unitless)\ndepth (m)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_768550_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_768550/index.htmlTable https://www.bco-dmo.org/dataset/768550 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_768550.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_768550&showErrors=false&email= BCO-DMO bcodmo_dataset_768550
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_753343.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_753343/ public Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016. These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.\n\ncdm_data_type = Other\nVARIABLES:\nGOLD_Project_ID (unitless)\nAnalysis_Project_Name (unitless)\nType (unitless)\nAssembly_Method (unitless)\nCollection_Date (unitless)\nInstrument (unitless)\nJGI_Contigs_Link (unitless)\nJGI_Project_ID (unitless)\nJGI_Sample_ID (unitless)\nJGI_Sequencing_Project_ID (unitless)\nJGI_Sequencing_Project_Name (unitless)\nLatitude_and_Longitude (Longitude, unitless)\nNCBI_BioProject_Accession (NCBI Bio Project Accession, unitless)\nNCBI_BioSample_Accession (NCBI Bio Sample Accession, unitless)\nNCBI_Project_ID (unitless)\nNCBI_SRA_Accession_ID (unitless)\nSample_Name (unitless)\nSequencing_Run_Mode (unitless)\nTotal_Bases (unitless)\nVolume_Seawater_Filtered (milliliters (mL))\nenv_biome (unitless)\n... (5 more variables)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_753343_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_753343/index.htmlTable https://www.bco-dmo.org/dataset/753343 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_753343.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_753343&showErrors=false&email= BCO-DMO bcodmo_dataset_753343
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518 https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745518/ public Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community.  Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503).  Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021.\\r\\n\\r\\nThese data were published in Hu et al. (2018).\n\ncdm_data_type = Other\nVARIABLES:\nSRA_run (unitless)\nSRA_run_link (unitless)\nSRA_study (unitless)\nbioproject_accession (unitless)\nbiosample_accession (unitless)\nlibrary_ID (unitless)\ntitle (unitless)\nsample_name (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfilename2 (unitless)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_745518_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745518/index.htmlTable https://www.bco-dmo.org/dataset/745518 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745518.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745518&showErrors=false&email= BCO-DMO bcodmo_dataset_745518
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.subset https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745527.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_745527/ public NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California.  Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014.  This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248).\n\ncdm_data_type = Other\nVARIABLES:\nbioproject_accession (unitless)\nsample_name (unitless)\nSRA_run_ID (unitless)\nSRA_run_link (unitless)\nlibrary_ID (unitless)\nSRA_study_ID (unitless)\nSRA_title (unitless)\nlibrary_strategy (unitless)\nlibrary_source (unitless)\nlibrary_selection (unitless)\nlibrary_layout (unitless)\nplatform (unitless)\ninstrument_model (unitless)\ndesign_description (unitless)\nfiletype (unitless)\nfilename (unitless)\nfiletpe2 (unitless)\nfilename2 (unitless)\ndepth2 (Depth, various)\nlatitude (degrees_north)\nlongitude (degrees_east)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_745527_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_745527/index.htmlTable https://www.bco-dmo.org/dataset/745527 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_745527.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_745527&showErrors=false&email= BCO-DMO bcodmo_dataset_745527
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817436 https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817436.graph https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_817436/ public SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018) To document the effects of storm-driven freshwater runoff on\\u00a0sponge-\nassociated microbiomes, we leveraged the heavy rainfall\\u00a0associated with\nTax Day Flooding (July 2016) and Hurricane Harvey\\u00a0(August 2017) to\ncharacterize sponge-associated bacterial communities\\u00a0at five time points:\nin July 2016 (at detection of the mortality\\u00a0event), one month after the\nmortality event (August 2016), immediately\\u00a0after Hurricane Harvey\n(September 2017), one month after Hurricane\\u00a0Harvey (October 2017), and\napproximately one year following Hurricane\\u00a0Harvey (October 2018).\n \nThese data contain Sequence Read Archive (SRA) and BioSample accession numbers\nassociated with BioProject\\u00a0PRJNA605902\n(see\\u00a0[https://www.ncbi.nlm.nih.gov/bioproject/605902](\\\\https://www.ncbi.nlm.nih.gov/bioproject/605902\\\\))\\u00a0at\nThe National Center for Biotechnology Information.\n\ncdm_data_type = Other\nVARIABLES:\nSample_Name (unitless)\nCollection_Date_Start (unitless)\nCollection_Date_End (unitless)\nDepth_min (Depth, meters (m))\ndepth (m)\nBank (unitless)\nSpecies (unitless)\nSRA (unitless)\nAccession (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_817436_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_817436/index.htmlTable https://www.bco-dmo.org/dataset/817436 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_817436.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_817436&showErrors=false&email= BCO-DMO bcodmo_dataset_817436
https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_789136 https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_789136/ public Synthesis of publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor samples from the Dorado outcrop, L\\u014d'ihi Seamount, North Pond, and Juan de Fuca Ridge flank To summarize crustal bacterial and archaeal taxa for this review, we synthesized publicly-available sequence datasets of the 16S rRNA gene in environmental DNA extracted from seafloor and subseafloor basalts generated using 454, Illumina and Ion Torrent amplicon platforms. These include seafloor basalts from the Dorado Outcrop and the L\\u014d'ihi Seamount in the Pacific Ocean and subseafloor basalts from North Pond on the western flank of the Mid-Atlantic Ridge and the Juan de Fuca Ridge flank in the northeastern Pacific Ocean. Datasets from rock colonization experiments conducted in the subseafloor at the Juan de Fuca Ridge flank site were also included, as well as microbial community surveys of the subseafloor crustal fluids from the anoxic Juan de Fuca site and the oxic North Pond site.\n\ncdm_data_type = Other\nVARIABLES:\nPlot_Order (unitless)\nSample_Name (unitless)\nSRA_Run (unitless)\nSRA_LibraryName (SRA Library Name, unitless)\nStudy_Nickname (unitless)\nSample_Type (unitless)\nTemp (Temperature, unitless)\nLocation (unitless)\ndepth2 (Depth, unitless)\nSequencer_Type (unitless)\nregion16S (Region16 S, unitless)\nPrimers (unitless)\nDNAextraction (unitless)\nDOI (unitless)\nSRA_Study (unitless)\n https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_789136_iso19115.xml https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_789136/index.htmlTable https://www.bco-dmo.org/dataset/789136 (external link) https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_789136.rss https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_789136&showErrors=false&email= BCO-DMO bcodmo_dataset_789136

 
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