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Dataset Title:  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)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_675040)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   Maximum ?
 specimen (unitless) ?          "sato1182"    "sato99"
 cruise_id (unitless) ?          "ANT-XXVII-2"    "UM-08-09"
 station (unitless) ?          4    184
 length (millimeters) ?          "10.6"    "N/D"
 SRA_accession (unitless) ?          "SRR4072782"    "SRR4072855"
 BioSample_accession (unitless) ?          "SAMN05604989"    "SAMN05605036"
 SRA_accession_link (unitless) ?          "    "
 BioSample_accession_link (unitless) ?          "    "
Server-side Functions ?
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  specimen {
    String bcodmo_name "sample";
    String description "salp specimen identifier";
    String long_name "Specimen";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  cruise_id {
    String bcodmo_name "cruise_id";
    String description "cruise identifier";
    String long_name "Cruise Id";
    String units "unitless";
  station {
    Int16 _FillValue 32767;
    Int16 actual_range 4, 184;
    String bcodmo_name "station";
    String description "station number";
    String long_name "Station";
    String units "unitless";
  length {
    String bcodmo_name "length";
    String description "salp length";
    String long_name "Length";
    String units "millimeters";
  SRA_accession {
    String bcodmo_name "accession number";
    String description "GenBank SRA accession number";
    String long_name "SRA Accession";
    String units "unitless";
  BioSample_accession {
    String bcodmo_name "accession number";
    String description "GenBank BioSample accession number";
    String long_name "Bio Sample Accession";
    String units "unitless";
  SRA_accession_link {
    String bcodmo_name "external_link";
    String description "GenBank SRA accession number with link to GenBank page";
    String long_name "SRA Accession Link";
    String units "unitless";
  BioSample_accession_link {
    String bcodmo_name "external_link";
    String description "GenBank BioSample accession number with link to GenBank page";
    String long_name "Bio Sample Accession Link";
    String units "unitless";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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)";
    String awards_0_award_nid "54892";
    String awards_0_award_number "ANT-1044982";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1044982";
    String awards_0_funder_name "NSF Antarctic Sciences";
    String awards_0_funding_acronym "NSF ANT";
    String awards_0_funding_source_nid "369";
    String awards_0_program_manager "Dr Peter Milne";
    String awards_0_program_manager_nid "51468";
    String cdm_data_type "Other";
    String comment 
"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>";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2017-01-17T20:14:47Z";
    String date_modified "2018-10-03T18:30:05Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.728225";
    String history 
"2024-07-23T12:32:46Z (local files)
2024-07-23T12:32:46Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_675040.html";
    String infoUrl "https://www.bco-dmo.org/dataset/675040";
    String institution "BCO-DMO";
    String instruments_0_acronym "MOC1";
    String instruments_0_dataset_instrument_nid "675051";
    String instruments_0_description "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).";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/NETT0097/";
    String instruments_0_instrument_name "MOCNESS1";
    String instruments_0_instrument_nid "437";
    String instruments_0_supplied_name "Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets";
    String instruments_1_acronym "TrawlMid";
    String instruments_1_dataset_instrument_nid "675052";
    String instruments_1_description 
"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.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/23/";
    String instruments_1_instrument_name "Midwater Trawl";
    String instruments_1_instrument_nid "467";
    String instruments_1_supplied_name "Rectangular Midwater Trawl (RMT 1+8)";
    String instruments_2_acronym "Automated Sequencer";
    String instruments_2_dataset_instrument_description "For genome sequencing";
    String instruments_2_dataset_instrument_nid "675068";
    String instruments_2_description "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.";
    String instruments_2_instrument_name "Automated DNA Sequencer";
    String instruments_2_instrument_nid "649";
    String instruments_2_supplied_name "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)";
    String instruments_3_acronym "IKMT";
    String instruments_3_dataset_instrument_nid "675053";
    String instruments_3_description 
"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).";
    String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/NETT0071/";
    String instruments_3_instrument_name "Isaacs-Kidd Midwater Trawl";
    String instruments_3_instrument_nid "715";
    String instruments_3_supplied_name "2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net";
    String instruments_4_acronym "Thermal Cycler";
    String instruments_4_dataset_instrument_description "A PCR product ∼500 bp was generated, followed by development of internal primers to produce a smaller PCR product amenable to qPCR.";
    String instruments_4_dataset_instrument_nid "675067";
    String instruments_4_description 
"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)";
    String instruments_4_instrument_name "PCR Thermal Cycler";
    String instruments_4_instrument_nid "471582";
    String instruments_5_acronym "Bioanalyzer";
    String instruments_5_dataset_instrument_description "For RNA quality control, and to assess the size distribution of library fragments.";
    String instruments_5_dataset_instrument_nid "675076";
    String instruments_5_description "A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.";
    String instruments_5_instrument_name "Bioanalyzer";
    String instruments_5_instrument_nid "626182";
    String instruments_5_supplied_name "Agilent 2100 Bioanalyzer";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/675040/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/675040";
    String param_mapping "{'675040': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/675040/parameters";
    String people_0_affiliation "University of Connecticut";
    String people_0_affiliation_acronym "UConn - Avery Point";
    String people_0_person_name "Ann Bucklin";
    String people_0_person_nid "50389";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of Connecticut";
    String people_1_affiliation_acronym "UConn";
    String people_1_person_name "Dr Rachel  J. O'Neill";
    String people_1_person_nid "51393";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Connecticut Sea Grant";
    String people_2_affiliation_acronym "CTSG";
    String people_2_person_name "Dr Diana Payne";
    String people_2_person_nid "51392";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Salp_Antarctic";
    String projects_0_acronym "Salp_Antarctic";
    String projects_0_description 
"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.";
    String projects_0_end_date "2014-05";
    String projects_0_geolocation "Southern Ocean";
    String projects_0_name "Population ecology of Salpa thompsoni based on molecular indicators";
    String projects_0_project_nid "2174";
    String projects_0_start_date "2011-06";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary 
"This dataset reports Salpa thompsoni specimens used for
genomics/transcriptomics with their GenBank accession links.
Related Dataset: [Salp sample log](\\\\https://www.bco-
    String title "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)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


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