http://lod.bco-dmo.org/id/dataset/675040
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-01-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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)
2017-01-27
publication
2017-01-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2018-02-23
publication
https://doi.org/10.1575/1912/bco-dmo.728225
Ann Bucklin
University of Connecticut
principalInvestigator
Rachel J. O'Neill
University of Connecticut
principalInvestigator
Diana Payne
Connecticut Sea Grant
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Bucklin, A., O'Neill, R., Payne, D. (2017) 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). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-01-27 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.728225 [access date]
Antarctic salp genome and RNAseq transcriptome Dataset Description: <p>This dataset reports Salpa thompsoni specimens used for genomics/transcriptomics with their GenBank accession links.</p>
<p><strong>Related Dataset:</strong> Salp sample log:&nbsp;www.bco-dmo.org/dataset/672600</p> Methods and Sampling: <p>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 335μm mesh nets; upper 200 m were sampled with a 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net.&nbsp;Western Antarctic Peninsula region, Southern Ocean (November-December 2011)</p>
<p>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)</p>
<p>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)</p>
Funding provided by NSF Antarctic Sciences (NSF ANT) Award Number: ANT-1044982 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1044982
completed
Ann Bucklin
University of Connecticut
860-405-9208
Avery Point Campus 1080 Shennecossett Rd.
Groton
CT
06340
USA
ann.bucklin@uconn.edu
pointOfContact
Rachel J. O'Neill
University of Connecticut
CT
06269
USA
pointOfContact
Diana Payne
Connecticut Sea Grant
860 405-9248
University of Connecticut - Avery Point 1080 Shennecossett Road
Groton
CT
06340-6048
diana.payne@uconn.edu
pointOfContact
asNeeded
Unknown
specimen
cruise_id
station
length
BioSample_accession
BioSample_accession_link
SRA_accession
SRA_accession_link
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)
Agilent 2100 Bioanalyzer
2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net
Rectangular Midwater Trawl (RMT 1+8)
Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets
theme
None, User defined
sample identification
Cruise identfier
station
length
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bioanalyzer
Isaacs-Kidd Midwater Trawl
Midwater Trawl
MOCNESS1
Thermal Cycler
instrument
BCO-DMO Standard Instruments
LMG1110
UM-08-09
ANT-XXVII-2
service
Deployment Activity
Southern Ocean
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Population ecology of Salpa thompsoni based on molecular indicators
https://osprey.bco-dmo.org/project/2174
Population ecology of Salpa thompsoni based on molecular indicators
<p>The Antarctic salp, <em>Salpa thompsoni</em>, 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 <em>S. thompsoni</em> in the Southern Ocean. The proposed next steps in our genomic/transcriptomic analysis of <em>Salpa thompsoni</em> 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 <em>S. thompsoni</em> in relation to the Antarctic pelagic ecosystem and extreme and variable environmental conditions of the Southern Ocean.</p>
<p>Most of the data from this project are available from the Marine Geoscience Data System (MGDS), part of IEDA and is available at <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=18148">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=18148</a>.</p>
Salp_Antarctic
largerWorkCitation
project
eng; USA
biota
oceans
Southern Ocean
-74.567
42.002
-66.183
-60.901
2009-01-12
2011-12-02
Southern Ocean
0
BCO-DMO catalogue of parameters from 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)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/675057.rdf
Name: specimen
Units: unitless
Description: <p>salp specimen identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/675058.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/675059.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/675060.rdf
Name: length
Units: millimeters
Description: <p>salp length</p>
http://lod.bco-dmo.org/id/dataset-parameter/675062.rdf
Name: BioSample_accession
Units: unitless
Description: <p>GenBank BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/675064.rdf
Name: BioSample_accession_link
Units: unitless
Description: <p>GenBank BioSample accession number with link to GenBank page</p>
http://lod.bco-dmo.org/id/dataset-parameter/676609.rdf
Name: SRA_accession
Units: unitless
Description: <p>GenBank SRA accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/676610.rdf
Name: SRA_accession_link
Units: unitless
Description: <p>GenBank SRA accession number with link to GenBank page</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
11994
https://darchive.mblwhoilibrary.org/bitstream/1912/9610/1/data_salp-genome-and-transcriptome.tsv
download
https://doi.org/10.1575/1912/bco-dmo.728225
download
onLine
dataset
<p>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 335μm mesh nets; upper 200 m were sampled with a 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net.&nbsp;Western Antarctic Peninsula region, Southern Ocean (November-December 2011)</p>
<p>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)</p>
<p>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)</p>
Specified by the Principal Investigator(s)
<p>Molecular genetic (genomic and transcriptomic) data resulting from this project have been submitted to appropriate sections of the NCBI GenBank database, as follows:</p>
<p>The Salpa thompsoni Whole Genome Shotgun project (see Jue et al., 2016) has been deposited at DDBJ/ENA/GenBank Genome section under the Accession No. MKHR00000000.&nbsp; The version described in this paper is version MKHR01000000. The genomic data include the final assembly and annotations, as well as all of the raw data files (genomic and small RNAs). Accession Nos. are assigned to the genomic data submission, as follows: SUBID, SUB1479239; BioProject, PRJNA318929; BioSample, SAMN04870323. The Salp Genome Bioproject information and data are available at <a href="https://www.ncbi.nlm.nih.gov/genome/?term=MKHR00000000" target="_blank">https://www.ncbi.nlm.nih.gov/genome/?term=MKHR00000000</a>.</p>
<p>The Salpa thompsoni Transcriptome Shotgun Assembly project (see Batta-Lona et al., 2016) has been deposited at DDBJ/ENA/GenBank under the Accession No. GFCC00000000. The version described in this paper is version GFCC01000000. The transcriptomic data includes raw sequencing data and alignment information. The Bioproject Accession No. is <a href="https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&amp;from_uid=279245" target="_blank">PRJNA279245</a>, which includes RNA-seq data from 48 field-collected specimens, which are assigned Biosample Accession Nos. SAMN05604989 - SAMN05605036. The Salp Transcriptome Bioproject information and data are available at <a href="https://www.ncbi.nlm.nih.gov/nuccore/GFCC00000000" target="_blank">https://www.ncbi.nlm.nih.gov/nuccore/GFCC00000000</a>.</p>
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added cruise deployment identifiers<br />
- removed SRA accessions from data display</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
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)
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)
PI Supplied Instrument 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) PI Supplied Instrument Description:For genome sequencing Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Agilent 2100 Bioanalyzer
Agilent 2100 Bioanalyzer
PI Supplied Instrument Name: Agilent 2100 Bioanalyzer PI Supplied Instrument Description:For RNA quality control, and to assess the size distribution of library fragments. Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument 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.
2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net
2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net
PI Supplied Instrument Name: 2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net Instrument Name: Isaacs-Kidd Midwater Trawl Instrument Short Name:IKMT Instrument 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). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0071/
Rectangular Midwater Trawl (RMT 1+8)
Rectangular Midwater Trawl (RMT 1+8)
PI Supplied Instrument Name: Rectangular Midwater Trawl (RMT 1+8) Instrument Name: Midwater Trawl Instrument Short Name:TrawlMid Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/23/
Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets
Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets
PI Supplied Instrument Name: Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets Instrument Name: MOCNESS1 Instrument Short Name:MOC1 Instrument 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). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
PI Supplied Instrument Name: PI Supplied Instrument Description:A PCR product ∼500 bp was generated, followed by development of internal primers to produce a smaller PCR product amenable to qPCR. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: LMG1110
LMG1110
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
LMG1110
Ann Bucklin
University of Connecticut
http://data.bcodmo.org/LMG11-10/LMG11-10_Cruise_Report_06dec11.pdf
Report describing LMG1110
Cruise: UM-08-09
UM-08-09
Community Standard Description
International Council for the Exploration of the Sea
Umitaka-Maru
vessel
Cruise: ANT-XXVII-2
ANT-XXVII-2
Community Standard Description
International Council for the Exploration of the Sea
R/V Polarstern
vessel
ANT-XXVII-2
Eberhard Fahrbach
Alfred Wegener Institute for Polar and Marine Research
http://dmoserv3.bco-dmo.org/data_docs/Salp_Antarctic/cruise-rpt_ANT-27-2_Fah2011b.pdf
Report describing ANT-XXVII-2
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
Community Standard Description
International Council for the Exploration of the Sea
Umitaka-Maru
vessel