ERDDAP > info > bcodmo_dataset_746654

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	graph		files	public	[Trichodesmium AHL metatranscriptomes_AE1409] - Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata (Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation)		I   M	background			BCO-DMO	bcodmo_dataset_746654

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	Samples were collected on cruise AE1409.\u00a0Trichodesmium colonies were obtained by net tow (130 micron mesh) and serially washed in sterile surface seawater. Clean colonies were then incubated with or without a cocktail of quorum sensing molecules. After four hours of incubation, colonies were placed onto filters and stored in liquid nitrogen until RNA was extracted and submitted for sequencing at the Columbia University Genome Center.\u00a0 Methods:\u00a0We extracted prokaryotic RNA from triplicate control and +AHL samples by first adding approximately 500 \u03bcL of glass beads to each cryotube and bead beating with a vortex adaptor for 5 minutes. We extracted total RNA using the yeast protocol from the Qiagen RNeasy Mini Kit with the added on-column DNase digestion using the RNase-free DNase Kit (Qiagen, Hilden, Germany). We processed DNase-treated total RNA through a MICROBEnrich kit following the manufacturer\u2019s instructions (ThermoFisher Scientific, Waltham, MA, USA). We removed ribosomal RNA using a Ribo-Zero Magnetic Kit optimized for bacteria (Illumina, San Diego, CA, USA) following the manufacturer\u2019s instructions. Finally, we purified the prokaryotic RNA extract using the RNeasy MinElute Cleanup Kit by following manufacturer instructions and eluting in 14 \u03bcL water (Qiagen). We pooled together triplicate samples, and pooled RNA extracts were quantified using the Take3 Nucleic Acid Quantification program and a Biotek plate reader. To further assess quality of pooled triplicate RNA samples, we used a BioAnalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). The JP Sulzberger Genome Center at Columbia University carried out RNA sequencing with a depth of 60 million paired end reads using an Illumina HiSeq protocol. Quality control:\u00a0We trimmed sequence reads and normalized following the Eel Pond Protocol for mRNAseq assembly. To obtain read counts for each sample, we mapped cleaned forward and reverse reads to metagenome assemblies from the same sampling locations that were previously characterized and clustered into orthologous groups (OGs). We carried out mapping using RSEM with the paired- end and Bowtie2 parameters. We summed counts for previously determined OGs for Trichodesmium and epibiont genome bins separately. We determined significant changes in OG relative abundance between control and +AHL samples by comparing control and sample treatments using a stringent empirical Bayes approach called Analysis of Sequence Counts (ASC). This approach evaluates the posterior probability associated with a given fold change across pooled triplicates, and performs similarly, but conservatively, on replicated and unreplicated sample datasets. \u00a0OGs were considered significantly higher or lower if they had a 95% or higher posterior probability of a fold change greater than 2 between treatment and control. Taxonomic relative abundance estimates for metagenome samples were previously calculated by multiplying the length of each contig in a genome bin by read mapping coverage, and then summing those values for all contigs. Please refer to the manuscript related to this metadata for more details and references.
attribute	NC_GLOBAL	awards_0_award_nid	String	565175
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1332898
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332898
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	Donald L. Rice
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	51467
attribute	NC_GLOBAL	awards_1_award_nid	String	565184
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1332912
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332912
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	Donald L. Rice
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	51467
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Trichodesmium AHL metatranscriptome accessions Alantic Explorer AE1409, PABST cruise, May 2014 S. Dyhrman (LDEO), B. Van Mooy (WHOI), K. Frischkorn (LDEO) version: 2018-09-21 Link to NCBI BioProject PRJNA450995: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA450995
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	2018-09-21T20:13:26Z
attribute	NC_GLOBAL	date_modified	String	2019-03-20T14:30:43Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.746654.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/746654
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Plankton Net
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	The net had 130 micron mesh and was used to collect Trichodesmium colonies.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	746665
attribute	NC_GLOBAL	instruments_0_description	String	A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/22/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Plankton Net
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	525
attribute	NC_GLOBAL	instruments_0_supplied_name	String	net
attribute	NC_GLOBAL	instruments_1_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	746667
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	Illumina Miseq platform
attribute	NC_GLOBAL	instruments_2_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	746666
attribute	NC_GLOBAL	instruments_2_description	String	General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute	NC_GLOBAL	instruments_2_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	471582
attribute	NC_GLOBAL	keywords	String	accession, assembly, bco, bco-dmo, biological, bioproject, bioproject_accession, biosample, biosample_accession, chemical, data, dataset, description, design, design_description, dmo, erddap, filename, filename2, filename3, filename4, filename5, filename6, filename7, filename8, filetype, instrument, instrument_model, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, management, model, oceanography, office, platform, preliminary, selection, source, strategy, title
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/746654/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/746654
attribute	NC_GLOBAL	param_mapping	String	{'746654': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/746654/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Lamont-Doherty Earth Observatory
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	LDEO
attribute	NC_GLOBAL	people_0_person_name	String	Sonya T. Dyhrman
attribute	NC_GLOBAL	people_0_person_nid	String	51101
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
attribute	NC_GLOBAL	people_1_person_name	String	Benjamin A.S. Van Mooy
attribute	NC_GLOBAL	people_1_person_nid	String	50975
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	Lamont-Doherty Earth Observatory
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	LDEO
attribute	NC_GLOBAL	people_2_person_name	String	Kyle R. Frischkorn
attribute	NC_GLOBAL	people_2_person_nid	String	746669
attribute	NC_GLOBAL	people_2_role	String	Student
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	Nancy Copley
attribute	NC_GLOBAL	people_3_person_nid	String	50396
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	P Processing by Tricho
attribute	NC_GLOBAL	projects_0_acronym	String	P Processing by Tricho
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Colonies of the cyanbacterium Trichodesmium are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both Trichodesmium and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of Trichodesmium N2 fixation. Trichodesmium colonies employ an arsenal of strategies to mitigate the effects of phosphorus limitation, and the consortia of epibiotic bacteria in the colonies may play a significant role in phosphorus acquisition. In this study, researchers from Woods Hole Oceanographic Institution and Columbia University will use metagenomic and metatranscriptomic sequencing to investigate how phosphorus metabolism is coordinated in Trichodesmium consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of Trichodesmium from a monospecific colony whose primary function is fixing CO2 and N2 toward a unique planktonic consortium with a diverse, complex, and highly coordinated overall metabolism that exerts profound control over the cycling of inorganic and organic nutrients in the oligotrophic upper ocean.
attribute	NC_GLOBAL	projects_0_end_date	String	2016-09
attribute	NC_GLOBAL	projects_0_geolocation	String	Western Tropical North Atlantic
attribute	NC_GLOBAL	projects_0_name	String	Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
attribute	NC_GLOBAL	projects_0_project_nid	String	565176
attribute	NC_GLOBAL	projects_0_start_date	String	2013-10
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	bioproject_accession,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype,assembly,filename5,filename6,filename7,filename8
attribute	NC_GLOBAL	summary	String	Trichodesmium is a marine, diazotrophic cyanobacterium that plays a central role in the biogeochemical cycling of carbon and nitrogen. Colonies ubiquitously co-occur with a diverse microbiome of heterotrophic bacteria. Here we show that manipulation of the microbiome with quorum sensing acyl homoserine lactone (AHL) molecules significantly modulated rates of N2 fixation by Trichodesmium collected from the western North Atlantic, with both positive and negative effects of varied magnitude. Changes in Trichodesmium N2 fixation did not clearly correlate with changes in microbiome composition or geochemical patterns. Metatranscriptome sequencing revealed significant changes in the relative abundance of microbiome transcripts encoding metabolic functions consistent with quorum sensing responses in model bacteria. There was little overlap in specific microbiome transcriptional responses to AHL addition between stations, and this variability in microbiome gene expression may underpin the heterogeneous changes in Trichodesmium N2 fixation. These data suggest the microbiome could play a large and previously overlooked role in modulating Trichodesmium N2 fixation. This metadata form describes the metatranscriptomic sequencing reads that were used in the study.
attribute	NC_GLOBAL	title	String	[Trichodesmium AHL metatranscriptomes_AE1409] - Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata (Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	bioproject_accession		String
attribute	bioproject_accession	bcodmo_name	String	accession number
attribute	bioproject_accession	description	String	collection of biological data related to a single initiative
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	code for accessing short read sequence data from 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
attribute	library_ID	description	String	sample name code
attribute	library_ID	long_name	String	Library ID
attribute	library_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	library_ID	units	String	unitless
variable	title		String
attribute	title	bcodmo_name	String	sample_descrip
attribute	title	description	String	description and type of the sample
attribute	title	long_name	String	Title
attribute	title	units	String	unitless
variable	library_strategy		String
attribute	library_strategy	bcodmo_name	String	unknown
attribute	library_strategy	description	String	type of sequencing performed to generate the sample
attribute	library_strategy	long_name	String	Library Strategy
attribute	library_strategy	units	String	unitless
variable	library_source		String
attribute	library_source	bcodmo_name	String	unknown
attribute	library_source	description	String	type of sequence data represented by the sample
attribute	library_source	long_name	String	Library Source
attribute	library_source	units	String	unitless
variable	library_selection		String
attribute	library_selection	bcodmo_name	String	unknown
attribute	library_selection	description	String	how reads were prescreened (unspecified indicates reads were not screened)
attribute	library_selection	long_name	String	Library Selection
attribute	library_selection	units	String	unitless
variable	library_layout		String
attribute	library_layout	bcodmo_name	String	unknown
attribute	library_layout	description	String	whether sequenced reads were single or paired-end
attribute	library_layout	long_name	String	Library Layout
attribute	library_layout	units	String	unitless
variable	platform		String
attribute	platform	bcodmo_name	String	instrument
attribute	platform	description	String	sequencing machine platform used to generate reads
attribute	platform	long_name	String	Platform
attribute	platform	units	String	unitless
variable	instrument_model		String
attribute	instrument_model	bcodmo_name	String	instrument
attribute	instrument_model	description	String	make and model of the sequencing machine platform used
attribute	instrument_model	long_name	String	Instrument Model
attribute	instrument_model	units	String	unitless
variable	design_description		String
attribute	design_description	bcodmo_name	String	unknown
attribute	design_description	description	String	quick methods description detailing how genetic material was prepared prior to sequencing
attribute	design_description	long_name	String	Design Description
attribute	design_description	units	String	unitless
variable	filetype		String
attribute	filetype	bcodmo_name	String	unknown
attribute	filetype	description	String	type of file the reads are stored as
attribute	filetype	long_name	String	Filetype
attribute	filetype	units	String	unitless
variable	assembly		double
attribute	assembly	_FillValue	double	NaN
attribute	assembly	bcodmo_name	String	unknown
attribute	assembly	description	String	whether or not there is a linked assembly (blank indicates that no assembly is provided)
attribute	assembly	long_name	String	Assembly
attribute	assembly	units	String	unitless
variable	filename		String
attribute	filename	bcodmo_name	String	file_name
attribute	filename	description	String	name of the first read file
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 the second read file
attribute	filename2	long_name	String	Filename2
attribute	filename2	units	String	unitless
variable	filename3		String
attribute	filename3	bcodmo_name	String	file_name
attribute	filename3	description	String	name of the third read file
attribute	filename3	long_name	String	Filename3
attribute	filename3	units	String	unitless
variable	filename4		String
attribute	filename4	bcodmo_name	String	file_name
attribute	filename4	description	String	name of the fourth read file
attribute	filename4	long_name	String	Filename4
attribute	filename4	units	String	unitless
variable	filename5		double
attribute	filename5	_FillValue	double	NaN
attribute	filename5	bcodmo_name	String	file_name
attribute	filename5	description	String	additional read file (if present)
attribute	filename5	long_name	String	Filename5
attribute	filename5	units	String	unitless
variable	filename6		double
attribute	filename6	_FillValue	double	NaN
attribute	filename6	bcodmo_name	String	file_name
attribute	filename6	description	String	additional read file (if present)
attribute	filename6	long_name	String	Filename6
attribute	filename6	units	String	unitless
variable	filename7		double
attribute	filename7	_FillValue	double	NaN
attribute	filename7	bcodmo_name	String	file_name
attribute	filename7	description	String	additional read file (if present)
attribute	filename7	long_name	String	Filename7
attribute	filename7	units	String	unitless
variable	filename8		double
attribute	filename8	_FillValue	double	NaN
attribute	filename8	bcodmo_name	String	file_name
attribute	filename8	description	String	additional read file (if present)
attribute	filename8	long_name	String	Filename8
attribute	filename8	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.