ERDDAP > info > bcodmo_dataset_719970

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
		data			files	public	Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study		I   M	background			BCO-DMO	bcodmo_dataset_719970

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	Published methodology in Landa et al., 2017, ISME Journal, in press. One liter samples were filtered through 2-um polycarbonate (PC) membranes to collect bacterial cells and flash-frozen in liquid nitrogen and stored at -80C. Filters were extracted for RNA by the acid phenol:chloroform:isoamylalcohol method. Potential traces of DNA were removed using the Turbo DNA-free kit (Invitrogen, Waltham, MA, USA). Samples were tested for residual DNA by a 40-cycle PCR targeting the 16S rRNA gene of R. pomeroyi. Samples were depleted of rRNA using custom probes for small and large subunit rRNA genes from all three microbes (Stewart et al., 2010). Libraries were prepared for two replicate cubitainers at 8 time points (16 samples) using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Wilmington, MA, USA) at the Georgia Genomics Facility (University of Georgia) and sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA). Reference cited: Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4: 896\u2013907. doi:[10.1038/ismej.2010.18](\\"https://dx.doi.org/10.1038/ismej.2010.18\\")
attribute	NC_GLOBAL	awards_0_award_nid	String	541254
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1342694
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1342694
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	Switch RNAseq Data PI: Mary Ann Moran (University of Georgia) Version: 29 November 2017 Note: Transcript counts are reported in TPM (transcripts per million). This is the number of transcript reads mapped to an individual gene for every million transcripts mapped to the entire genome.
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	2017-11-27T20:45:13Z
attribute	NC_GLOBAL	date_modified	String	2020-01-14T16:35:14Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.719970.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/719970
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	Transcripts were sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA).
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	720063
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	bco, bco-dmo, biological, chemical, data, dataset, day12, Day12_R1, Day12_R2, day15, Day15_R1, Day15_R2, day18, Day18_R1, Day18_R2, day23, Day23_R1, Day23_R2, day30, Day30_R1, Day30_R2, day37, Day37_R1, Day37_R2, day7, Day7_R1, Day7_R2, day9, Day9_R1, Day9_R2, description, dmo, erddap, locus, Locus_Tag, management, oceanography, office, preliminary, tag
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/719970/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/719970
attribute	NC_GLOBAL	param_mapping	String	{'719970': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/719970/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	Shannon Rauch
attribute	NC_GLOBAL	people_1_person_nid	String	51498
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	OceanSulfurFluxBact
attribute	NC_GLOBAL	projects_0_acronym	String	OceanSulfurFluxBact
attribute	NC_GLOBAL	projects_0_description	String	Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling. The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation. This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-12
attribute	NC_GLOBAL	projects_0_name	String	Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
attribute	NC_GLOBAL	projects_0_project_nid	String	541255
attribute	NC_GLOBAL	projects_0_start_date	String	2014-01
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	summary	String	Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study. This dataset contains the processed, QC'ed, normalized sequence data. The full raw data file is deposited in the NCBI BioProject database under accession PRJNA381627.
attribute	NC_GLOBAL	title	String	Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	Locus_Tag		String
attribute	Locus_Tag	bcodmo_name	String	sample
attribute	Locus_Tag	description	String	gene identifier
attribute	Locus_Tag	long_name	String	Locus Tag
attribute	Locus_Tag	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Locus_Tag	units	String	unitless
variable	Description		String
attribute	Description	bcodmo_name	String	brief_desc
attribute	Description	description	String	gene function, if known
attribute	Description	long_name	String	Description
attribute	Description	units	String	unitless
variable	Day7_R1		String
attribute	Day7_R1	bcodmo_name	String	count
attribute	Day7_R1	description	String	Transcript count by day and replicate: day 7, replicate 1
attribute	Day7_R1	long_name	String	Day7 R1
attribute	Day7_R1	units	String	TPM (transcripts per million)
variable	Day7_R2		String
attribute	Day7_R2	bcodmo_name	String	count
attribute	Day7_R2	description	String	Transcript count by day and replicate: day 7, replicate 2
attribute	Day7_R2	long_name	String	Day7 R2
attribute	Day7_R2	units	String	TPM (transcripts per million)
variable	Day9_R1		String
attribute	Day9_R1	bcodmo_name	String	count
attribute	Day9_R1	description	String	Transcript count by day and replicate: day 9, replicate 1
attribute	Day9_R1	long_name	String	Day9 R1
attribute	Day9_R1	units	String	TPM (transcripts per million)
variable	Day9_R2		String
attribute	Day9_R2	bcodmo_name	String	count
attribute	Day9_R2	description	String	Transcript count by day and replicate: day 9, replicate 2
attribute	Day9_R2	long_name	String	Day9 R2
attribute	Day9_R2	units	String	TPM (transcripts per million)
variable	Day12_R1		String
attribute	Day12_R1	bcodmo_name	String	count
attribute	Day12_R1	description	String	Transcript count by day and replicate: day 12, replicate 1
attribute	Day12_R1	long_name	String	Day12 R1
attribute	Day12_R1	units	String	TPM (transcripts per million)
variable	Day12_R2		String
attribute	Day12_R2	bcodmo_name	String	count
attribute	Day12_R2	description	String	Transcript count by day and replicate: day 12, replicate 2
attribute	Day12_R2	long_name	String	Day12 R2
attribute	Day12_R2	units	String	TPM (transcripts per million)
variable	Day15_R1		String
attribute	Day15_R1	bcodmo_name	String	count
attribute	Day15_R1	description	String	Transcript count by day and replicate: day 15, replicate 1
attribute	Day15_R1	long_name	String	Day15 R1
attribute	Day15_R1	units	String	TPM (transcripts per million)
variable	Day15_R2		String
attribute	Day15_R2	bcodmo_name	String	count
attribute	Day15_R2	description	String	Transcript count by day and replicate: day 15, replicate 2
attribute	Day15_R2	long_name	String	Day15 R2
attribute	Day15_R2	units	String	TPM (transcripts per million)
variable	Day18_R1		String
attribute	Day18_R1	bcodmo_name	String	count
attribute	Day18_R1	description	String	Transcript count by day and replicate: day 18, replicate 1
attribute	Day18_R1	long_name	String	Day18 R1
attribute	Day18_R1	units	String	TPM (transcripts per million)
variable	Day18_R2		String
attribute	Day18_R2	bcodmo_name	String	count
attribute	Day18_R2	description	String	Transcript count by day and replicate: day 18, replicate 2
attribute	Day18_R2	long_name	String	Day18 R2
attribute	Day18_R2	units	String	TPM (transcripts per million)
variable	Day23_R1		String
attribute	Day23_R1	bcodmo_name	String	count
attribute	Day23_R1	description	String	Transcript count by day and replicate: day 23, replicate 1
attribute	Day23_R1	long_name	String	Day23 R1
attribute	Day23_R1	units	String	TPM (transcripts per million)
variable	Day23_R2		String
attribute	Day23_R2	bcodmo_name	String	count
attribute	Day23_R2	description	String	Transcript count by day and replicate: day 23, replicate 2
attribute	Day23_R2	long_name	String	Day23 R2
attribute	Day23_R2	units	String	TPM (transcripts per million)
variable	Day30_R1		String
attribute	Day30_R1	bcodmo_name	String	count
attribute	Day30_R1	description	String	Transcript count by day and replicate: day 30, replicate 1
attribute	Day30_R1	long_name	String	Day30 R1
attribute	Day30_R1	units	String	TPM (transcripts per million)
variable	Day30_R2		String
attribute	Day30_R2	bcodmo_name	String	count
attribute	Day30_R2	description	String	Transcript count by day and replicate: day 30, replicate 2
attribute	Day30_R2	long_name	String	Day30 R2
attribute	Day30_R2	units	String	TPM (transcripts per million)
variable	Day37_R1		String
attribute	Day37_R1	bcodmo_name	String	count
attribute	Day37_R1	description	String	Transcript count by day and replicate: day 37, replicate 1
attribute	Day37_R1	long_name	String	Day37 R1
attribute	Day37_R1	units	String	TPM (transcripts per million)
variable	Day37_R2		String
attribute	Day37_R2	bcodmo_name	String	count
attribute	Day37_R2	description	String	Transcript count by day and replicate: day 37, replicate 2
attribute	Day37_R2	long_name	String	Day37 R2
attribute	Day37_R2	units	String	TPM (transcripts per million)

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.