ERDDAP > info > bcodmo_dataset_739636

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data			files	public	[Thaumarchaea transcriptomes] - Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. (Gene content, gene expression, and physiology in mesopelagic ammonia- oxidizing archaea)		I   M	background			BCO-DMO	bcodmo_dataset_739636

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	Thaumarchaea transcriptomes sequences.
attribute	NC_GLOBAL	awards_0_award_nid	String	555306
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1259994
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1259994
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	awards_1_award_nid	String	555311
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1260006
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260006
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Thaumarchaea transcriptomes C. Dupont & A. Santoro, PIs Version 10 July 2018
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	date_created	String	2018-07-10T18:08:40Z
attribute	NC_GLOBAL	date_modified	String	2019-06-12T13:34:50Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.739636.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/739636
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to identify samples
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	739746
attribute	NC_GLOBAL	instruments_0_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_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina NextSEQ 500
attribute	NC_GLOBAL	keywords	String	accession, bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, management, name, oceanography, office, organism, preliminary, sample, Sample_Name, strain, tax, Tax_ID
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/739636/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/739636
attribute	NC_GLOBAL	param_mapping	String	{'739636': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/739636/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	J. Craig Venter Institute
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	JCVI
attribute	NC_GLOBAL	people_0_person_name	String	Christopher Dupont
attribute	NC_GLOBAL	people_0_person_nid	String	555309
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 California-Santa Barbara
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UCSB
attribute	NC_GLOBAL	people_1_person_name	String	Alyson Santoro
attribute	NC_GLOBAL	people_1_person_nid	String	555313
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	J. Craig Venter Institute
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	JCVI
attribute	NC_GLOBAL	people_2_person_name	String	Christopher Dupont
attribute	NC_GLOBAL	people_2_person_nid	String	555309
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	Hannah Ake
attribute	NC_GLOBAL	people_3_person_nid	String	650173
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	AmoA Archaea
attribute	NC_GLOBAL	projects_0_acronym	String	AmoA Archaea
attribute	NC_GLOBAL	projects_0_description	String	NSF award abstract: Intellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's "twilight zone" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically: 1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations 2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies The investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle. Broader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-03
attribute	NC_GLOBAL	projects_0_geolocation	String	Epipelagic and mesopelagic, Equatorial Pacific
attribute	NC_GLOBAL	projects_0_name	String	Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
attribute	NC_GLOBAL	projects_0_project_nid	String	555307
attribute	NC_GLOBAL	projects_0_start_date	String	2013-04
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	Organism,Tax_ID
attribute	NC_GLOBAL	summary	String	Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.
attribute	NC_GLOBAL	title	String	[Thaumarchaea transcriptomes] - Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. (Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	Accession		String
attribute	Accession	bcodmo_name	String	accession number
attribute	Accession	description	String	Accession number and NCBI link
attribute	Accession	long_name	String	Accession
attribute	Accession	units	String	unitless
variable	Sample_Name		String
attribute	Sample_Name	bcodmo_name	String	sample
attribute	Sample_Name	description	String	Sample name
attribute	Sample_Name	long_name	String	Sample Name
attribute	Sample_Name	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Sample_Name	units	String	unitless
variable	Organism		String
attribute	Organism	bcodmo_name	String	species
attribute	Organism	description	String	Species of organism
attribute	Organism	long_name	String	Organism
attribute	Organism	units	String	unitless
variable	Tax_ID		int
attribute	Tax_ID	_FillValue	int	2147483647
attribute	Tax_ID	actual_range	int	1410606, 1410606
attribute	Tax_ID	bcodmo_name	String	sample
attribute	Tax_ID	description	String	Taxonomic identification
attribute	Tax_ID	long_name	String	Tax ID
attribute	Tax_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Tax_ID	units	String	unitless
variable	Strain		String
attribute	Strain	bcodmo_name	String	sample
attribute	Strain	description	String	Strain identification
attribute	Strain	long_name	String	Strain
attribute	Strain	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Strain	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.