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     data        files  public 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)
   ?     I   M   background (external link) RSS 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 (external link)
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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.2d 13 Jun 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 &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.728225
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/675040 (external link)
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/ (external link)
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/ (external link)
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/ (external link)
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 �m 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, identifier, length, link, management, oceanography, office, preliminary, sample, specimen, sra, SRA_accession, SRA_accession_link, station
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/675040 (external link)
attribute NC_GLOBAL param_mapping String {'675040': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/675040/parameters (external link)
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 Dr 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 Population ecology of Salpa thompsoni based on molecular indicators
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 http://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 Nancy Copley
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
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 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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable specimen   String  
attribute specimen description String salp specimen identifier
attribute specimen ioos_category String Unknown
attribute specimen long_name String Specimen
attribute specimen units String unitless
variable cruise_id   String  
attribute cruise_id description String cruise identifier
attribute cruise_id ioos_category String 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 description String station number
attribute station ioos_category String Identifier
attribute station long_name String Station
attribute station units String unitless
variable length   String  
attribute length description String salp length
attribute length ioos_category String Unknown
attribute length long_name String Length
attribute length units String millimeters
variable SRA_accession   String  
attribute SRA_accession description String GenBank SRA accession number
attribute SRA_accession ioos_category String Unknown
attribute SRA_accession long_name String SRA Accession
attribute SRA_accession units String unitless
variable BioSample_accession   String  
attribute BioSample_accession description String GenBank BioSample accession number
attribute BioSample_accession ioos_category String Unknown
attribute BioSample_accession long_name String Bio Sample Accession
attribute BioSample_accession units String unitless
variable SRA_accession_link   String  
attribute SRA_accession_link description String GenBank SRA accession number with link to GenBank page
attribute SRA_accession_link ioos_category String Unknown
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 description String GenBank BioSample accession number with link to GenBank page
attribute BioSample_accession_link ioos_category String Unknown
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, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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