Accessing BCO-DMO data
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BCO-DMO ERDDAP
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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_998887_v1 | https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_998887_v1.graph | https://erddap.bco-dmo.org/erddap/files/bcodmo_dataset_998887_v1/ | public | [SAGs from the Pacific Ocean OMZ] - Single-cell amplified genomes (SAGs) collected during CTD casts in the Eastern Tropical Pacific Ocean on R/V Atlantis cruise AT50-08 during February-March 2023 (Collaborative Research: Microdiversity drives ecosystem function: SAR11 bacteria as models for oceanic nitrogen loss) | This dataset describes assembled genomes of single-cell amplified genomes (SAGs) used in Zhao et al., ISME 2025. Water samples were collected during conductivity–temperature–depth (CTD) casts from an oxygen minimum zone in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community, during the R/V Atlantis cruise AT50-08. Sorting was performed on 4 April 2023 (within 2 months from the date the first sample was collected) and SAGs were generated with the modified genomic DNA amplification technique, WGA-Y, which enables a substantially improved average genome recovery from single cells (serviceS-202). In total, 105 SAGs with Cp values<3h were randomly selected for sequencing. Genome assembly and draft annotation were performed by Single Cell Genomics Facility (SCGC), Maine, USA as described in the center's webpage https://scgc.bigelow.org/capabilities/service-description/ and in the Zhao et al., paper. The single-cell amplified genomes are available in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA1124867.\n\ncdm_data_type = Other\nVARIABLES:\nSAG_identifier (unitless)\nStation (unitless)\nlatitude (degrees_north)\nlongitude (degrees_east)\ndepth (m)\nCollection_date (unitless)\nGenome (unitless)\nClade (unitless)\nCompleteness (ranging from 0 to 100%)\nContamination (ranging from 0 to 100%)\nStrain_heterogeneity (ranging from 0 to 100%)\nExperiment_Accession (unitless)\nStudy_Accession (unitless)\nSample_Accession (unitless)\nSAG_ID (unitless)\n | https://erddap.bco-dmo.org/erddap/metadata/fgdc/xml/bcodmo_dataset_998887_v1_fgdc.xml | https://erddap.bco-dmo.org/erddap/metadata/iso19115/xml/bcodmo_dataset_998887_v1_iso19115.xml | https://erddap.bco-dmo.org/erddap/info/bcodmo_dataset_998887_v1/index.htmlTable | https://osprey.bco-dmo.org/dataset/998887
| https://erddap.bco-dmo.org/erddap/rss/bcodmo_dataset_998887_v1.rss | https://erddap.bco-dmo.org/erddap/subscriptions/add.html?datasetID=bcodmo_dataset_998887_v1&showErrors=false&email= | BCO-DMO | bcodmo_dataset_998887_v1 | |||
| log in | [Subsurface Nitrospirota and Nitrospinota Origins] - Collection of subsurface bacteria Nitrospirota and Nitrospinota genome data including IMG and NCBI accessions for sequence datasets in June 2021 (Slow Life in Crust project) (Microbial activity in the crustal deep biosphere) | The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique mitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. We used phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species tree reconciliation methods to investigate the life histories of these two phyla. This dataset includes list of previously-published sequence datasets that were used for the analysis. The data and interpretations are published at DOI 10.1038/s41396-023-01397-x. Additional metadata such as NCBI accessions, assembly release dates, and NCBI taxon ids were added in December 2024.\n\ncdm_data_type = Other\nVARIABLES:\nID (unitless)\nIMG_genome_id (unitless)\nGenBank_assembly (unitless)\nSample (unitless)\nCorrected_BioSample (unitless)\nBioProject (unitless)\nrelease_date (unitless)\nlast_updated_date (seconds since 1970-01-01T00:00:00Z)\npublication_date (seconds since 1970-01-01T00:00:00Z)\nDomain (unitless)\nPhylum (unitless)\nClass (unitless)\nOrder (unitless)\nFamily (unitless)\nGenus (unitless)\nSpecies (unitless)\nNCBI_organism_taxid (unitless)\nIsolation_Source (unitless)\nIsolationPlot (unitless)\n... (11 more variables)\n | BCO-DMO | bcodmo_dataset_933610_v1 |