ERDDAP > info > bcodmo_dataset_818765

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	[Diatom Matrix RNAseq] - Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture (Metabolic Currencies of the Ocean Carbon Cycle)		I   M	background			BCO-DMO	bcodmo_dataset_818765

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	Thalassiosira pseudonana were removed from the co-cultures by pre-filtration through 2.0 \u00b5m pore-size filters, and bacteria were collected on 0.2 \u00b5m pore-size filters. Filters were incubated in SDS (0.6% final concentration) and proteinase K (120 ng \u03bcl \u20131 final concentration). RNA was extracted from duplicates of each treatment by adding an equal volume of acid phenol:chloroform:isoamyl-alcohol, followed by shaking, centrifugation, and collection of the supernatant. A second extraction was carried out by the addition of an equal volume of chloroform:isoamyl-alcohol. RNA was recovered from the supernatant, treated to remove rRNA, and sequenced. Each sequence library is from four independent bacterial samples that were pooled for sequencing. The data are assigned to one of the four samples post- sequencing by mapping to the genomes of each of the four bacteria. The data table provides the accession numbers of the bacterial genomes to be used for mapping in the final column.
attribute	NC_GLOBAL	awards_0_award_nid	String	765520
attribute	NC_GLOBAL	awards_0_award_number	String	IOS-1656311
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1656311
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Integrative Organismal Systems
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF IOS
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	626136
attribute	NC_GLOBAL	awards_0_program_manager	String	Mamta Rawat
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	765519
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Diatom Matrix RNAseq NCBI accessions for transcriptome data for bacteria collected 8 hrs after individual inoculation into a diatom Thalassiosira psuedonana culture. PI: M. A. Moran (UGA) version date: 2020-07-16
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	2020-07-16T14:58:37Z
attribute	NC_GLOBAL	date_modified	String	2020-07-20T20:17:45Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.818765.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/818765
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	818797
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	HiSeq Illumina 2500
attribute	NC_GLOBAL	keywords	String	accession, bco, bco-dmo, bio, biological, bioproject, BioSample, chemical, data, dataset, description, dmo, erddap, genome, management, microbe, name, ncbi, NCBI_Bioproject_Accession, NCBI_Genome_Accession, oceanography, office, preliminary, replicate, sample, Sample_Name, taxon, taxon_microbe
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/818765/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/818765
attribute	NC_GLOBAL	param_mapping	String	{'818765': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/818765/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Georgia
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UGA
attribute	NC_GLOBAL	people_0_person_name	String	Mary Ann Moran
attribute	NC_GLOBAL	people_0_person_nid	String	51592
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	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_1_person_name	String	Nancy Copley
attribute	NC_GLOBAL	people_1_person_nid	String	50396
attribute	NC_GLOBAL	people_1_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	project	String	Metabolic Currencies
attribute	NC_GLOBAL	projects_0_acronym	String	Metabolic Currencies
attribute	NC_GLOBAL	projects_0_description	String	NSF Award Abstract: The roles of microbes in cycling carbon and nutrients in the ocean - the largest biological system on Earth - were initially described about 40 years ago. Now, it is known that half of Earth's primary production is carried out by marine phytoplankton, and half of that is recycled within weeks by marine bacteria. This proposal is a collaboration between microbiologists and chemists to identify the specific compounds that pass between phytoplankton and bacteria in surface ocean waters. Identifying the key chemicals of the ocean's microbial food web will provide insights into how the marine carbon cycle is regulated, generate data to improve ocean carbon models, and train new scientists at the interface of microbiology and chemistry. Hands-on learning opportunities in microbial ecology will be provided for high school students, both in the classroom and in marine ecosystems of the Georgia coast. Phytoplankton metabolites that sustain the flow of carbon between microbial autotrophs and heterotrophs in the surface ocean carbon cycle will be identified in this project. A matrix of model systems consisting of bacteria-phytoplankton co-cultures will be used as biological assays for key metabolites based on expression patterns of bacterial transporter genes. The chemical identity of candidate metabolites and evaluation of their potential ecological role will be carried out by exometabolomic analysis of co-cultures with bacterial transporter mutants. Both advanced mass spectrometry and NMR will be used for metabolomics analysis, taking advantage of the sensitivity and compound identification strengths of each. The distribution of candidate metabolites in the ocean microbiome and other microbial systems will be characterized by mining environmental sequence datasets for orthologous transporter genes. This project represents a novel approach to identifying metabolites important in microbiome function, compounds often difficult to address with standard chemical approaches because of their low concentrations and high biological demand.
attribute	NC_GLOBAL	projects_0_end_date	String	2020-06
attribute	NC_GLOBAL	projects_0_name	String	Metabolic Currencies of the Ocean Carbon Cycle
attribute	NC_GLOBAL	projects_0_project_nid	String	765521
attribute	NC_GLOBAL	projects_0_start_date	String	2017-07
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	NCBI_Bioproject_Accession
attribute	NC_GLOBAL	summary	String	Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168.
attribute	NC_GLOBAL	title	String	[Diatom Matrix RNAseq] - Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture (Metabolic Currencies of the Ocean Carbon Cycle)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Sample_Name		String
attribute	Sample_Name	bcodmo_name	String	sample
attribute	Sample_Name	description	String	sample identifier
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	NCBI_Bioproject_Accession		String
attribute	NCBI_Bioproject_Accession	bcodmo_name	String	accession number
attribute	NCBI_Bioproject_Accession	description	String	NCBI Bioproject accession number
attribute	NCBI_Bioproject_Accession	long_name	String	NCBI Bioproject Accession
attribute	NCBI_Bioproject_Accession	units	String	unitless
variable	BioSample		String
attribute	BioSample	bcodmo_name	String	accession number
attribute	BioSample	description	String	NCBI Biosample accession number
attribute	BioSample	long_name	String	Bio Sample
attribute	BioSample	units	String	unitless
variable	Description		String
attribute	Description	bcodmo_name	String	sample_descrip
attribute	Description	description	String	Description of sample
attribute	Description	long_name	String	Description
attribute	Description	units	String	unitless
variable	replicate		byte
attribute	replicate	_FillValue	byte	127
attribute	replicate	actual_range	byte	1, 2
attribute	replicate	bcodmo_name	String	replicate
attribute	replicate	description	String	Replicate number
attribute	replicate	long_name	String	Replicate
attribute	replicate	units	String	unitless
variable	NCBI_Genome_Accession		String
attribute	NCBI_Genome_Accession	bcodmo_name	String	accession number
attribute	NCBI_Genome_Accession	description	String	NCBI Genome accession number
attribute	NCBI_Genome_Accession	long_name	String	NCBI Genome Accession
attribute	NCBI_Genome_Accession	units	String	unitless
variable	taxon_microbe		String
attribute	taxon_microbe	bcodmo_name	String	taxon
attribute	taxon_microbe	description	String	Microbial identification
attribute	taxon_microbe	long_name	String	Taxon Microbe
attribute	taxon_microbe	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.