ERDDAP > info > bcodmo_dataset_675040

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
		data			files	public	[Salp genome and transcriptome] - Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) (Population ecology of Salpa thompsoni based on molecular indicators)		I   M	background			BCO-DMO	bcodmo_dataset_675040

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	1) Cruise R/V LM GOULD (LMG1110): Samples collected using Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335\u03bcm mesh nets; upper 200 m were sampled with a 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 \u00b5m mesh net.\u00a0Western Antarctic Peninsula region, Southern Ocean (November- December 2011) 2) Cruise R/V Polarstern (PS-ANT-XVII/2): Samples collected using a Rectangular Midwater Trawl (RMT 1+8) from the upper 200 m. Western Antarctic Peninsula region, Southern Ocean (January 2011) 3) Cruise R/V Umitaka Maru (UM-08-09): Samples collected using a RMT 1+8 from 2,000 m to surface. Indian Sector, Southern Ocean (January 2009)
attribute	NC_GLOBAL	awards_0_award_nid	String	54892
attribute	NC_GLOBAL	awards_0_award_number	String	ANT-1044982
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1044982
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Antarctic Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF ANT
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	369
attribute	NC_GLOBAL	awards_0_program_manager	String	Dr Peter Milne
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	51468
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Salpa thompsoni genome and transcriptone accessions PI: A. Bucklin (UConn) version: 2017-01-27 (SRA numbers and links added) replaces version 2017-01-06 NOTE: These data were published in Supplementary Table 1, Batta-Lona et al (2016) Pol. Bio. doi:10.1007/s00300-016-2051-6 For complete information, see GenBank BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/279245" target="_blank">BioProject 279245</a>
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	2017-01-17T20:14:47Z
attribute	NC_GLOBAL	date_modified	String	2018-10-03T18:30:05Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.728225
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/675040
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	MOC1
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	675051
attribute	NC_GLOBAL	instruments_0_description	String	The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003).
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	MOCNESS1
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	437
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets
attribute	NC_GLOBAL	instruments_1_acronym	String	TrawlMid
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	675052
attribute	NC_GLOBAL	instruments_1_description	String	A mid-water or pelagic trawl is a net towed at a chosen depth in the water column to catch schooling fish such as herring and mackerel. Midwater trawl nets have very large front openings to herd schooling fish toward the back end where they become trapped in the narrow "broiler". The sides of the deployed net are spread horizontally with two large metal foils, called "doors," positioned in front of the net. As the trawler moves forward, the doors, and therefore the net, are forced outward, keeping the net open. This instrument designation is used when specific make and model are not known.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/23/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Midwater Trawl
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	467
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Rectangular Midwater Trawl (RMT 1+8)
attribute	NC_GLOBAL	instruments_2_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	For genome sequencing
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	675068
attribute	NC_GLOBAL	instruments_2_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_2_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_2_supplied_name	String	Multiple sequencing platforms: Ion Torrent Proton (Life Technologies, Grand Island, NY), a 454 FLX WGS (Roche Applied Science, Branford, CT), and an Illumina HiSeq 200 (Illumina, San Diego, CA)
attribute	NC_GLOBAL	instruments_3_acronym	String	IKMT
attribute	NC_GLOBAL	instruments_3_dataset_instrument_nid	String	675053
attribute	NC_GLOBAL	instruments_3_description	String	A trawl with a pentagonal mouth opening and a dihedral depressor vane as part of the mouth opening. IKMTs come in various dimensions (refer to individual dataset documentation). The original IKMTs were 10 foot (304 cm) and 15 foot (457 cm) at the mouth. The 10 foot IKMT net was 31 feet (9.45 m) in length (Wiebe and Benfield 2003).
attribute	NC_GLOBAL	instruments_3_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/NETT0071/
attribute	NC_GLOBAL	instruments_3_instrument_name	String	Isaacs-Kidd Midwater Trawl
attribute	NC_GLOBAL	instruments_3_instrument_nid	String	715
attribute	NC_GLOBAL	instruments_3_supplied_name	String	2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net
attribute	NC_GLOBAL	instruments_4_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_4_dataset_instrument_description	String	A PCR product ∼500 bp was generated, followed by development of internal primers to produce a smaller PCR product amenable to qPCR.
attribute	NC_GLOBAL	instruments_4_dataset_instrument_nid	String	675067
attribute	NC_GLOBAL	instruments_4_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_4_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_4_instrument_nid	String	471582
attribute	NC_GLOBAL	instruments_5_acronym	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_5_dataset_instrument_description	String	For RNA quality control, and to assess the size distribution of library fragments.
attribute	NC_GLOBAL	instruments_5_dataset_instrument_nid	String	675076
attribute	NC_GLOBAL	instruments_5_description	String	A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
attribute	NC_GLOBAL	instruments_5_instrument_name	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_5_instrument_nid	String	626182
attribute	NC_GLOBAL	instruments_5_supplied_name	String	Agilent 2100 Bioanalyzer
attribute	NC_GLOBAL	keywords	String	accession, bco, bco-dmo, bio, biological, BioSample_accession, BioSample_accession_link, chemical, cruise, cruise_id, data, dataset, dmo, erddap, length, link, management, oceanography, office, preliminary, sample, specimen, sra, SRA_accession, SRA_accession_link, station
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/675040/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/675040
attribute	NC_GLOBAL	param_mapping	String	{'675040': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/675040/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Connecticut
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UConn - Avery Point
attribute	NC_GLOBAL	people_0_person_name	String	Ann Bucklin
attribute	NC_GLOBAL	people_0_person_nid	String	50389
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 Connecticut
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UConn
attribute	NC_GLOBAL	people_1_person_name	String	Dr Rachel J. O'Neill
attribute	NC_GLOBAL	people_1_person_nid	String	51393
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	Connecticut Sea Grant
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	CTSG
attribute	NC_GLOBAL	people_2_person_name	String	Dr Diana Payne
attribute	NC_GLOBAL	people_2_person_nid	String	51392
attribute	NC_GLOBAL	people_2_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_2_role_type	String	originator
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	Salp_Antarctic
attribute	NC_GLOBAL	projects_0_acronym	String	Salp_Antarctic
attribute	NC_GLOBAL	projects_0_description	String	The Antarctic salp, Salpa thompsoni, is an increasingly important player in the vulnerable Antarctic Peninsula pelagic ecosystem. Observations of high abundance of Salpa thompsoni during the summer in the Southern Ocean suggest that this species is capable of rapid somatic and population growth, and frequently forms dense blooms under favorable environmental conditions. The proposed research will examine genome-wide patterns of gene expression, target gene expression levels, and patterns of population genetic diversity and structure of the target salp species. Our preliminary results and data analysis have provided a promising basis for transcriptomic studies of S. thompsoni in the Southern Ocean. The proposed next steps in our genomic/transcriptomic analysis of Salpa thompsoni are: 1) completion of a reference transcriptome as a basis for genome-wide analysis of gene expression; 2) whole transcriptome shotgun sequencing (RNA-Seq) analysis to characterize gene expression in relation to individual characteristics and environmental conditions; 3) quantitative real-time PCR (qRT-PCR) characterization and validation of gene expression for 10-20 top differentially-expressed genes; and 4) detection of strand-specific allelic variation at SNP (Single Nucleotide Polymorphic) sites to analyze clonal diversity and population genetic diversity and structure. We hypothesize that: 1) deep analysis of the Salpa thompsoni transcriptome will reveal significant associations among selected set of differentially-expressed genes and critical life history stages and events (e.g., ontogenetic maturation, sexual reproduction, senescence) of the salp; and 2) the species will show variable levels of clonal diversity and significant genetic differentiation among salp populations in different regions of the Southern Ocean. Samples will be obtained from research cruises during 2011-2013 in diverse regions of the Southern Ocean; dedicated sample and data collection will be carried out during a cruise of the R/V LM GOULD (LMG11-10) to the Western Antarctic Peninsula region in November, 2011. The significance of this effort lies in new understanding of the molecular processes underlying the complex life history and population dynamics of S. thompsoni in relation to the Antarctic pelagic ecosystem and extreme and variable environmental conditions of the Southern Ocean. Most of the data from this project are available from the Marine Geoscience Data System (MGDS), part of IEDA and is available at https://www.marine-geo.org/tools/search/Files.php?data_set_uid=18148.
attribute	NC_GLOBAL	projects_0_end_date	String	2014-05
attribute	NC_GLOBAL	projects_0_geolocation	String	Southern Ocean
attribute	NC_GLOBAL	projects_0_name	String	Population ecology of Salpa thompsoni based on molecular indicators
attribute	NC_GLOBAL	projects_0_project_nid	String	2174
attribute	NC_GLOBAL	projects_0_start_date	String	2011-06
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	This dataset reports Salpa thompsoni specimens used for genomics/transcriptomics with their GenBank accession links. Related Dataset: [Salp sample log](\\https://www.bco- dmo.org/dataset/672600\\)
attribute	NC_GLOBAL	title	String	[Salp genome and transcriptome] - Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) (Population ecology of Salpa thompsoni based on molecular indicators)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	specimen		String
attribute	specimen	bcodmo_name	String	sample
attribute	specimen	description	String	salp specimen identifier
attribute	specimen	long_name	String	Specimen
attribute	specimen	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	specimen	units	String	unitless
variable	cruise_id		String
attribute	cruise_id	bcodmo_name	String	cruise_id
attribute	cruise_id	description	String	cruise identifier
attribute	cruise_id	long_name	String	Cruise Id
attribute	cruise_id	units	String	unitless
variable	station		short
attribute	station	_FillValue	short	32767
attribute	station	actual_range	short	4, 184
attribute	station	bcodmo_name	String	station
attribute	station	description	String	station number
attribute	station	long_name	String	Station
attribute	station	units	String	unitless
variable	length		String
attribute	length	bcodmo_name	String	length
attribute	length	description	String	salp length
attribute	length	long_name	String	Length
attribute	length	units	String	millimeters
variable	SRA_accession		String
attribute	SRA_accession	bcodmo_name	String	accession number
attribute	SRA_accession	description	String	GenBank SRA accession number
attribute	SRA_accession	long_name	String	SRA Accession
attribute	SRA_accession	units	String	unitless
variable	BioSample_accession		String
attribute	BioSample_accession	bcodmo_name	String	accession number
attribute	BioSample_accession	description	String	GenBank BioSample accession number
attribute	BioSample_accession	long_name	String	Bio Sample Accession
attribute	BioSample_accession	units	String	unitless
variable	SRA_accession_link		String
attribute	SRA_accession_link	bcodmo_name	String	external_link
attribute	SRA_accession_link	description	String	GenBank SRA accession number with link to GenBank page
attribute	SRA_accession_link	long_name	String	SRA Accession Link
attribute	SRA_accession_link	units	String	unitless
variable	BioSample_accession_link		String
attribute	BioSample_accession_link	bcodmo_name	String	external_link
attribute	BioSample_accession_link	description	String	GenBank BioSample accession number with link to GenBank page
attribute	BioSample_accession_link	long_name	String	Bio Sample Accession Link
attribute	BioSample_accession_link	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.