http://lod.bco-dmo.org/id/dataset/622522
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
2015-10-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill project)
2016-05-04
publication
2016-05-04
revision
BCO-DMO Linked Data URI
2016-05-04
creation
http://lod.bco-dmo.org/id/dataset/622522
Peter H. Wiebe
Woods Hole Oceanographic Institution
principalInvestigator
Ann Bucklin
University of Connecticut
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: Wiebe, P. H., Bucklin, A. (2016) Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 3) Version Date 2016-05-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/622522 [access date]
Euphausiid DNA barcode metadata and accession numbers from global oceans Dataset Description: <p>Euphausiid DNA barcode metadata and accession numbers for DNA sequences for mitochondrial cytochrome oxidase I (COI) barcode regions. Specimens were collected in the Red Sea, Atlantic and Pacific Oceans.</p> Methods and Sampling: <p>Specimens of each of the five euphausiid species identified from the alcohol-preserved samples were prepared for PCR amplification and DNA sequencing. DNA sequences for the COI barcode region were determined for Euphausia diomedeae (4 individuals); E. sanzoi (2); E. sibogae (4); Stylocheiron abbreviatum (3); and S. affine (4). The designated GenBank Accession Numbers can be used to access the GenBank records, which include data and metadata for all specimens (Table 2). Additional specimens of each species (except Euphausia sanzoi) were identified from archived samples from cruises in the NE Pacific; NW, NE, and SE Atlantic; and Arabian Sea (Fig. 4), and were analyzed using the same methods.</p>
<p>DNA was purified from individual euphausiids using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) using standard protocols, except that elution volumes were reduced usually to 100-200 µL. A ~708 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene was amplified using consensus primers (Folmer et al., 1994) and published PCR amplification protocols (Bucklin et al., 2010b). The PCR products were run on 2% agarose gels and purified using the QIAquick Gel Extraction Kit (QIAGEN) following the manufacturer’s instructions, with an elution volume of 35 µL. DNA sequencing was done using a commercial service (Eurofins MWG Operon, Louisville, KY) following all protocols and instructions provided.<br />
<br />
See "Related Datasets" for data that can be joined to this dataset using the column "tow."</p>
Funding provided by King Abdullah University of Science and Technology (KAUST) Award Number: KAUST-Kaartvedt-2014
onGoing
Peter H. Wiebe
Woods Hole Oceanographic Institution
508-289-2313
Biology Department Redfield 2-26 MS #33
Woods Hole
MA
02543-1049
USA
pwiebe@whoi.edu
pointOfContact
Ann Bucklin
University of Connecticut
860-405-9208
Avery Point Campus 1080 Shennecossett Rd.
Groton
CT
06340
USA
ann.bucklin@uconn.edu
pointOfContact
asNeeded
Dataset Version: 3
Unknown
species
voucher_num
NCBI_accession
region
date
lat
lon
depth_range
cruise_id
station
tow
net
comment
inst
MOC-25
MOC-1
theme
None, User defined
species scientific name (binomial)
sample identification
accession number
region
date
latitude
longitude
depth_range
Cruise identfier
station
tow
net
comments
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Midwater Trawl
MOCNESS.25
MOCNESS1
Reeve Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Thuwal-2014-01
NH1208
OC473
ANT-XXIV_1
RHB0603
TT045
AKES-2
service
Deployment Activity
Red Sea
transect between 35 and 50N along CLIVAR line P17N
western North Atlantic, 35-50 degrees North
Sargasso Sea and Southeast North Atlantic Ocean
U.S. JGOFS Arabian Sea
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.
Red Sea Krill
https://osprey.bco-dmo.org/project/620092
Red Sea Krill
<p>The krill population at station ECDEEP was characterized via MOCNESS sampling and CTD casts.</p>
Red Sea Krill
largerWorkCitation
project
eng; USA
biota
oceans
Red Sea; transect between 35 and 50N along CLIVAR line P17N; western North Atlantic, 35-50 degrees North; Sargasso Sea and Southeast North Atlantic Ocean; U.S. JGOFS Arabian Sea
2016-05-04
Red Sea
0
BCO-DMO catalogue of parameters from Euphausiid DNA barcode metadata and accession numbers collected from cruises in the Red Sea, the western North Atlantic, the Sargasso Sea, the Southeast North Atlantic Ocean, and Arabian Sea (Red Sea Krill 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/622531.rdf
Name: species
Units: unitless
Description: <p>Euphausiid species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/622532.rdf
Name: voucher_num
Units: unitless
Description: <p>Bucklin lab specimen voucher number</p>
http://lod.bco-dmo.org/id/dataset-parameter/622533.rdf
Name: NCBI_accession
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/622534.rdf
Name: region
Units: unitless
Description: <p>geographical area of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/622535.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>date collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/622536.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/622537.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/622538.rdf
Name: depth_range
Units: meters
Description: <p>depth range sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/643634.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/643635.rdf
Name: station
Units: unitless
Description: <p>sequential station</p>
http://lod.bco-dmo.org/id/dataset-parameter/643636.rdf
Name: tow
Units: unitless
Description: <p>tow identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/643637.rdf
Name: net
Units: unitless
Description: <p>net number</p>
http://lod.bco-dmo.org/id/dataset-parameter/643638.rdf
Name: comment
Units: unitless
Description: <p>comments</p>
http://lod.bco-dmo.org/id/dataset-parameter/644711.rdf
Name: inst
Units: dimensionless
Description: <p>type of gear used to sample zooplankton: MOC-1 = MOCNESS-1meter; MOC-25 = MOCNESS-1/4 meter; </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
16578
https://datadocs.bco-dmo.org/file/7DDMxlYfJ8vX/krill_barcodes_v3.csv
krill_barcodes_v3.csv
Primary data file for dataset ID 622522
download
https://osprey.bco-dmo.org/dataset/622522/data/download
download
onLine
dataset
<p>Specimens of each of the five euphausiid species identified from the alcohol-preserved samples were prepared for PCR amplification and DNA sequencing. DNA sequences for the COI barcode region were determined for Euphausia diomedeae (4 individuals); E. sanzoi (2); E. sibogae (4); Stylocheiron abbreviatum (3); and S. affine (4). The designated GenBank Accession Numbers can be used to access the GenBank records, which include data and metadata for all specimens (Table 2). Additional specimens of each species (except Euphausia sanzoi) were identified from archived samples from cruises in the NE Pacific; NW, NE, and SE Atlantic; and Arabian Sea (Fig. 4), and were analyzed using the same methods.</p>
<p>DNA was purified from individual euphausiids using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) using standard protocols, except that elution volumes were reduced usually to 100-200 µL. A ~708 base-pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene was amplified using consensus primers (Folmer et al., 1994) and published PCR amplification protocols (Bucklin et al., 2010b). The PCR products were run on 2% agarose gels and purified using the QIAquick Gel Extraction Kit (QIAGEN) following the manufacturer’s instructions, with an elution volume of 35 µL. DNA sequencing was done using a commercial service (Eurofins MWG Operon, Louisville, KY) following all protocols and instructions provided.<br />
<br />
See "Related Datasets" for data that can be joined to this dataset using the column "tow."</p>
Specified by the Principal Investigator(s)
<p>DNA sequences were manually checked for accurate machine reading using the Molecular Evolutionary Genetics Analysis (MEGA, Ver. 6) software package (Tamura et al., 2013). DNA sequences to be analyzed were aligned and forward and reverse reads were reconciled using CLUSTAL-W, as implemented in MEGA (Thompson et al., 1997). MegaBLAST searches were conducted in GenBank to confirm the accuracy and validity of the sequences. DNA sequences that could not be verified and validated, including aberrant or highly divergent sequences, were omitted from the dataset. Published DNA sequences for the COI barcode region were obtained from GenBank (see e.g., Bucklin et al., 2007) and included in the sequence alignment for comparative analysis. Both the original alignment and an alignment trimmed to a 500 bp region in common among all sequences were used. In the latter case, any sequence shorter than the target 500 bp region was removed from further analysis, with the exception of several shorter sequences for Red Sea specimens.</p>
<p>A pairwise distance matrix showing within and between species differences (p-distances) for all sequences was determined and mean and standard deviations for within and between species were calculated. Pairwise p-distances were visually displayed as heat maps. A Neighbor Joining tree analysis was carried out in MEGA Ver.6 (Tamura et al., 2013) with Kimura-2-Parameter distances (a = 0.5). Node support was obtained after 1,000 bootstraps.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- replaced space with underscore</p>
<p>2016-04-27 revision: [replaces version: 2015-10-28]<br />
- added live links to NCBI GenBank, columns for cruise_id, station, tow, and net</p>
<p>2016-05-04: added links to MOC-CTD data from other BCO-DMO datasets, where available</p>
<p>&nbsp;</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
PI Supplied Instrument Name: 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.
PI Supplied Instrument Name: PI Supplied Instrument Description:a Krill trawl with a 38 m2 mouth area, and with a Multisampler unit attached to the rear end. The Multisampler unit has five nets mounted on a frame, similar to the MOCNESS, and is also remotely controlled. Also called a "Macroplankton Trawl".
Heino, M., Porteiro, F.M., Sutton, T.T., Falkenhaug, T., Godø, O.R., and Piatkowski, U. (2011) Catchability of pelagic trawls for sampling deep-living nekton in the mid-North Atlantic. ICES Journal of Marine Science 68, 377–389.
Krafft, B.A., Melle, W., Knutsen, T., Bagøien, E., Broms, C., Ellertsen, B., Siegel, V., (2010) Distribution and demography of Antarctic krill in the Southeast Atlantic sector of the Southern Ocean during the austral summer 2008. Polar Biology 33, 957–968. 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/
MOC-25
MOC-25
PI Supplied Instrument Name: MOC-25 Instrument Name: MOCNESS.25 Instrument Short Name:MOC.25 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-1/4 carries nine 1/4-m2 nets usually of 64 micrometer mesh and is used to sample the larger micro-zooplankton. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
MOC-1
MOC-1
PI Supplied Instrument Name: MOC-1 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: Instrument Name: Reeve Net Instrument Short Name:Reeve Net Instrument Description: A Reeve Net is a conventional ring net with a very large acrylic cylindrical cod-end (30 liters) designed to collect fragile gelatinous animals. The net is lowered to a particular depth and then hauled slowly back to the surface (5-10 m/min). Reeve (1981) also described a double net system with no bridle and flotation at the net mouth that is attached to a roller mechanism that rides on a tow wire.
The roller system is locked in place by a pressure release device. Once below a set pressure, the roller
and nets are released and they float slowly up the wire, gently collecting the zooplankton, without being
influenced by the motion of the vessel and associated vertical wire movements. (from Wiebe and Benfield, 2003) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0147/
PI Supplied Instrument Name: 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: Thuwal-2014-01
Thuwal-2014-01
R/V Thuwal
R/V Thuwal
vessel
Thuwal-2014-01
Peter H. Wiebe
Woods Hole Oceanographic Institution
Cruise: NH1208
NH1208
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
NH1208
Gareth Lawson
Woods Hole Oceanographic Institution
http://hdl.handle.net/1834/43090
Report describing NH1208
Cruise: OC473
OC473
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC473
Gareth Lawson
Woods Hole Oceanographic Institution
http://hdl.handle.net/1834/43091
Report describing OC473
Cruise: ANT-XXIV_1
ANT-XXIV_1
Community Standard Description
International Council for the Exploration of the Sea
R/V Polarstern
vessel
ANT-XXIV_1
Dr Sigi Schiel
Alfred Wegener Institute for Polar and Marine Research
http://epic.awi.de/28985/1/Sch2009ad.pdf
Report describing ANT-XXIV_1
Cruise: RHB0603
RHB0603
Community Standard Description
International Council for the Exploration of the Sea
NOAA Ship Ronald H. Brown
vessel
RHB0603
Peter H. Wiebe
Woods Hole Oceanographic Institution
http://www.cmarz.org/CMarZ_RHBrown_April06/Cruise_Report/working.htm
Report describing RHB0603
Cruise: TT045
TT045
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TT045
John F. Marra
Lamont-Doherty Earth Observatory
Cruise: AKES-2
AKES-2
R/V GO_Sars
Community Standard Description
International Council for the Exploration of the Sea
R/V GO_Sars
vessel
AKES-2
Dr Webjørn Melle
Institute of Marine Research (Bergen, Norway)
http://dmoserv3.bco-dmo.org/data_docs/Red_Sea_Krill/cruise_Surveyreport_AKES-2_270508.pdf
Report describing AKES-2
R/V Thuwal
R/V Thuwal
vessel
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
Community Standard Description
International Council for the Exploration of the Sea
R/V Polarstern
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
R/V GO_Sars
Community Standard Description
International Council for the Exploration of the Sea
R/V GO_Sars
vessel