ERDDAP > info > bcodmo_dataset_745518

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data			files	public	Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015		I   M	background			BCO-DMO	bcodmo_dataset_745518

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv
attribute	NC_GLOBAL	acquisition_description	String	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.
attribute	NC_GLOBAL	awards_0_award_nid	String	743048
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1737409
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1737409
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Microbial eukaryotic focused metatranscriptome data PI: David Caron Data version 2: 2020-02-26
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2018-09-04T20:19:13Z
attribute	NC_GLOBAL	date_modified	String	2020-05-11T22:00:05Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.745518.2
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/745518
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	773599
attribute	NC_GLOBAL	instruments_0_description	String	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.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	413
attribute	NC_GLOBAL	instruments_1_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503).
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	745534
attribute	NC_GLOBAL	instruments_1_description	String	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.
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_1_supplied_name	String	HiSeq
attribute	NC_GLOBAL	keywords	String	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
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/745518/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/745518
attribute	NC_GLOBAL	param_mapping	String	{'745518': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/745518/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Southern California
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	USC
attribute	NC_GLOBAL	people_0_person_name	String	David Caron
attribute	NC_GLOBAL	people_0_person_nid	String	50524
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	University of Southern California
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	USC
attribute	NC_GLOBAL	people_1_person_name	String	Sarah K. Hu
attribute	NC_GLOBAL	people_1_person_nid	String	745520
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	University of Southern California
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	USC
attribute	NC_GLOBAL	people_2_person_name	String	Sarah K. Hu
attribute	NC_GLOBAL	people_2_person_nid	String	745520
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Amber D. York
attribute	NC_GLOBAL	people_3_person_nid	String	643627
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	SPOT
attribute	NC_GLOBAL	projects_0_acronym	String	SPOT
attribute	NC_GLOBAL	projects_0_description	String	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.
attribute	NC_GLOBAL	projects_0_end_date	String	2021-07
attribute	NC_GLOBAL	projects_0_geolocation	String	San Pedro Channel off the coast of Los Angeles
attribute	NC_GLOBAL	projects_0_name	String	Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
attribute	NC_GLOBAL	projects_0_project_nid	String	743049
attribute	NC_GLOBAL	projects_0_start_date	String	2017-08
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype
attribute	NC_GLOBAL	summary	String	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).
attribute	NC_GLOBAL	title	String	Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015
attribute	NC_GLOBAL	version	String	2
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	SRA_run		String
attribute	SRA_run	bcodmo_name	String	accession number
attribute	SRA_run	description	String	SRA Run identifier at NCBI
attribute	SRA_run	long_name	String	SRA Run
attribute	SRA_run	units	String	unitless
variable	SRA_run_link		String
attribute	SRA_run_link	bcodmo_name	String	external_link
attribute	SRA_run_link	description	String	URL for SRA Run Page at NCBI
attribute	SRA_run_link	long_name	String	SRA Run Link
attribute	SRA_run_link	units	String	unitless
variable	SRA_study		String
attribute	SRA_study	bcodmo_name	String	accession number
attribute	SRA_study	description	String	SRA study identifier at NCBI
attribute	SRA_study	long_name	String	SRA Study
attribute	SRA_study	units	String	unitless
variable	bioproject_accession		String
attribute	bioproject_accession	bcodmo_name	String	accession number
attribute	bioproject_accession	description	String	BioProject accesion number at NCBI
attribute	bioproject_accession	long_name	String	Bioproject Accession
attribute	bioproject_accession	units	String	unitless
variable	biosample_accession		String
attribute	biosample_accession	bcodmo_name	String	accession number
attribute	biosample_accession	description	String	BioSample accession number at NCBI
attribute	biosample_accession	long_name	String	Biosample Accession
attribute	biosample_accession	units	String	unitless
variable	library_ID		String
attribute	library_ID	bcodmo_name	String	sample_descrip
attribute	library_ID	description	String	SRA title
attribute	library_ID	long_name	String	Library ID
attribute	library_ID	units	String	unitless
variable	title		String
attribute	title	bcodmo_name	String	sample_descrip
attribute	title	description	String	Descriptive title of SRA accession
attribute	title	long_name	String	Title
attribute	title	units	String	unitless
variable	sample_name		String
attribute	sample_name	bcodmo_name	String	sample_descrip
attribute	sample_name	description	String	Sample name
attribute	sample_name	long_name	String	Sample Name
attribute	sample_name	units	String	unitless
variable	library_strategy		String
attribute	library_strategy	bcodmo_name	String	sample_descrip
attribute	library_strategy	description	String	Library strategy ("AMPLICON")
attribute	library_strategy	long_name	String	Library Strategy
attribute	library_strategy	units	String	unitless
variable	library_source		String
attribute	library_source	bcodmo_name	String	sample_descrip
attribute	library_source	description	String	Library source ("TRANSCRIPTOMIC" or "GENOMIC")
attribute	library_source	long_name	String	Library Source
attribute	library_source	units	String	unitless
variable	library_selection		String
attribute	library_selection	bcodmo_name	String	sample_descrip
attribute	library_selection	description	String	Library selection ("PCR")
attribute	library_selection	long_name	String	Library Selection
attribute	library_selection	units	String	unitless
variable	library_layout		String
attribute	library_layout	bcodmo_name	String	sample_descrip
attribute	library_layout	description	String	Library layout ("paired")
attribute	library_layout	long_name	String	Library Layout
attribute	library_layout	units	String	unitless
variable	platform		String
attribute	platform	bcodmo_name	String	sample_descrip
attribute	platform	description	String	Sequencing platform ("Illumina")
attribute	platform	long_name	String	Platform
attribute	platform	units	String	unitless
variable	instrument_model		String
attribute	instrument_model	bcodmo_name	String	sample_descrip
attribute	instrument_model	description	String	Sequencing instrument model ("Illumina MiSeq")
attribute	instrument_model	long_name	String	Instrument Model
attribute	instrument_model	units	String	unitless
variable	design_description		String
attribute	design_description	bcodmo_name	String	sample_descrip
attribute	design_description	description	String	Sequencing design description
attribute	design_description	long_name	String	Design Description
attribute	design_description	units	String	unitless
variable	filetype		String
attribute	filetype	bcodmo_name	String	sample_descrip
attribute	filetype	description	String	Type of files
attribute	filetype	long_name	String	Filetype
attribute	filetype	units	String	unitless
variable	filename		String
attribute	filename	bcodmo_name	String	file_name
attribute	filename	description	String	Name of file 1 (see NCBI for access)
attribute	filename	long_name	String	Filename
attribute	filename	units	String	unitless
variable	filename2		String
attribute	filename2	bcodmo_name	String	file_name
attribute	filename2	description	String	Name of file 2 (see NCBI for access)
attribute	filename2	long_name	String	Filename2
attribute	filename2	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.