Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_745518) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
SRA_run {
String bcodmo_name "accession number";
String description "SRA Run identifier at NCBI";
String long_name "SRA Run";
String units "unitless";
}
SRA_run_link {
String bcodmo_name "external_link";
String description "URL for SRA Run Page at NCBI";
String long_name "SRA Run Link";
String units "unitless";
}
SRA_study {
String bcodmo_name "accession number";
String description "SRA study identifier at NCBI";
String long_name "SRA Study";
String units "unitless";
}
bioproject_accession {
String bcodmo_name "accession number";
String description "BioProject accesion number at NCBI";
String long_name "Bioproject Accession";
String units "unitless";
}
biosample_accession {
String bcodmo_name "accession number";
String description "BioSample accession number at NCBI";
String long_name "Biosample Accession";
String units "unitless";
}
library_ID {
String bcodmo_name "sample_descrip";
String description "SRA title";
String long_name "Library ID";
String units "unitless";
}
title {
String bcodmo_name "sample_descrip";
String description "Descriptive title of SRA accession";
String long_name "Title";
String units "unitless";
}
sample_name {
String bcodmo_name "sample_descrip";
String description "Sample name";
String long_name "Sample Name";
String units "unitless";
}
library_strategy {
String bcodmo_name "sample_descrip";
String description "Library strategy (\"AMPLICON\")";
String long_name "Library Strategy";
String units "unitless";
}
library_source {
String bcodmo_name "sample_descrip";
String description "Library source (\"TRANSCRIPTOMIC\" or \"GENOMIC\")";
String long_name "Library Source";
String units "unitless";
}
library_selection {
String bcodmo_name "sample_descrip";
String description "Library selection (\"PCR\")";
String long_name "Library Selection";
String units "unitless";
}
library_layout {
String bcodmo_name "sample_descrip";
String description "Library layout (\"paired\")";
String long_name "Library Layout";
String units "unitless";
}
platform {
String bcodmo_name "sample_descrip";
String description "Sequencing platform (\"Illumina\")";
String long_name "Platform";
String units "unitless";
}
instrument_model {
String bcodmo_name "sample_descrip";
String description "Sequencing instrument model (\"Illumina MiSeq\")";
String long_name "Instrument Model";
String units "unitless";
}
design_description {
String bcodmo_name "sample_descrip";
String description "Sequencing design description";
String long_name "Design Description";
String units "unitless";
}
filetype {
String bcodmo_name "sample_descrip";
String description "Type of files";
String long_name "Filetype";
String units "unitless";
}
filename {
String bcodmo_name "file_name";
String description "Name of file 1 (see NCBI for access)";
String long_name "Filename";
String units "unitless";
}
filename2 {
String bcodmo_name "file_name";
String description "Name of file 2 (see NCBI for access)";
String long_name "Filename2";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Seawater was collected 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. Briefly, seawater was pre-filtered (80 mm) into 20 L carboys to
minimize the presence of multicellular eukaryotes. Replicate samples (ranging
in volume from 1.5-3.5 L) from each depth were filtered onto sterile GF/F
filters (nominal pore size 0.7 mm, Whatman, International Ltd. Florham Park,
NJ). While we cannot avoid some impact that sample handling (i.e., bringing
samples to the surface) may have had on our results, filters were immediately
placed in 1.5 mL of lysis buffer and flash frozen in liquid nitrogen in < 40
min and away from light to minimize RNA degradation.
Total RNA was extracted from each filter using a DNA/RNA AllPrep kit (Qiagen,
Valencia, CA, #80204) with an in-line genomic DNA removal step (RNase-free
DNase reagents, Qiagen #79254) (dx.doi.org/10.17504/protocols.io.hk3b4yn).
Extracted RNA was quality checked and low biomass samples were pooled. Six
replicates were processed and sequenced from the surface, while pairs of
filters were pooled for either 150 or 890 m, yielding 3 and 4 replicates
respectively (Supporting Information Table S1). RNA concentrations were
normalized before library preparation (Supporting Information). ERCC spike-in
was added before sequence library preparation with Kapa\\u2019s Stranded mRNA
library preparation kit using poly-A tail selection beads to select for
eukaryotic mRNA (Kapa Biosystems, Inc., Wilmington, MA, #KK8420).
Also see:
[https://www.protocols.io/view/sample-collection-from-the-field-for-
downs...](\\\\\"https://www.protocols.io/view/sample-collection-from-the-field-
for-downstream-mo-hisb4eehttps://www.protocols.io/view/rna-and-optional-dna-
extraction-from-environmental-hk3b4yn\\\\\")
The associated assembly files can be found at Zenodo (see Hu, S. K. (2017),
DOI:\\u00a010.5281/zenodo.1202041).\\u00a0 The assembly files were also
published in the journal publication Hu, et al. (2018).
Related code can be found in the github repository
[https://github.com/shu251/SPOT_metatranscriptome.\\u00a0](\\\\\"https://github.com/shu251/SPOT_metatranscriptome.\\\\u00a0\\\\\")
The version of the code used for these publications can be found in the
Supplemental Files section of this page.";
String awards_0_award_nid "743048";
String awards_0_award_number "OCE-1737409";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1737409";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Microbial eukaryotic focused metatranscriptome data
PI: David Caron
Data version 2: 2020-02-26";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String dataset_current_state "Final and no updates";
String date_created "2018-09-04T20:19:13Z";
String date_modified "2020-05-11T22:00:05Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.745518.2";
String history
"2024-04-26T15:32:55Z (local files)
2024-04-26T15:32:55Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_745518.html";
String infoUrl "https://www.bco-dmo.org/dataset/745518";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_nid "773599";
String instruments_0_description "A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
String instruments_0_instrument_name "Niskin bottle";
String instruments_0_instrument_nid "413";
String instruments_1_acronym "Automated Sequencer";
String instruments_1_dataset_instrument_description "HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503).";
String instruments_1_dataset_instrument_nid "745534";
String instruments_1_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_1_instrument_name "Automated DNA Sequencer";
String instruments_1_instrument_nid "649";
String instruments_1_supplied_name "HiSeq";
String keywords "accession, bco, bco-dmo, biological, bioproject, bioproject_accession, biosample, biosample_accession, chemical, data, dataset, description, design, design_description, dmo, erddap, filename, filename2, filetype, instrument, instrument_model, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, link, management, model, name, oceanography, office, platform, preliminary, run, sample, sample_name, selection, source, sra, SRA_run, SRA_run_link, SRA_study, strategy, study, title";
String license "https://www.bco-dmo.org/dataset/745518/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/745518";
String param_mapping "{'745518': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/745518/parameters";
String people_0_affiliation "University of Southern California";
String people_0_affiliation_acronym "USC";
String people_0_person_name "David Caron";
String people_0_person_nid "50524";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Southern California";
String people_1_affiliation_acronym "USC";
String people_1_person_name "Sarah K. Hu";
String people_1_person_nid "745520";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Southern California";
String people_2_affiliation_acronym "USC";
String people_2_person_name "Sarah K. Hu";
String people_2_person_nid "745520";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Amber D. York";
String people_3_person_nid "643627";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "SPOT";
String projects_0_acronym "SPOT";
String projects_0_description
"Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.
This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.";
String projects_0_end_date "2021-07";
String projects_0_geolocation "San Pedro Channel off the coast of Los Angeles";
String projects_0_name "Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series";
String projects_0_project_nid "743049";
String projects_0_start_date "2017-08";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype";
String summary "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).";
String title "Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015";
String version "2";
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.