http://lod.bco-dmo.org/id/dataset/666389
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
2016-11-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Link to NCBI BioProject on programmed cell death from RVIB Nathaniel B. Palmer NBP1302 in the Ross Sea from February to April 2013 (TRACERS project)
2016-11-30
publication
2016-11-30
revision
BCO-DMO Linked Data URI
2016-11-30
creation
http://lod.bco-dmo.org/id/dataset/666389
Monica V. Orellana
Institute for Systems Biology
principalInvestigator
Adrian Lopez Garcia de Lomana
Institute for Systems Biology
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
documentDigital
Cite this dataset as: Orellana, M. V., Lopez Garcia de Lomana, A. (2016) Link to NCBI BioProject on programmed cell death from RVIB Nathaniel B. Palmer NBP1302 in the Ross Sea from February to April 2013 (TRACERS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-11-30 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/666389 [access date]
Ross Sea sequences link Dataset Description: Methods and Sampling: <p>Sampling:<br />
Water samples collected during the cruise aboard the research vessel icebreaker (RV/IB) Nathaniel B. Palmer, as part of the&nbsp;TRacing&nbsp;the fate of Algal Carbon Export in the Ross Sea (TRACERS) program included nutrients (nitrate, nitrite, silica, phosphate, DOC, DIC, dC13, ). Samples for biological measurements were collected using a rosette sampler fitted with 20 12 L Niskin bottles (General Oceanics), a conductivity, temperature, and depth (CTD) sensor (Sea-Bird Electronics), an SBE 43 dissolved oxygen sensor, and a fluorometer (WET Labs). All seawater samples were stored immediately within 1 h of collection using HDPE amber bottles and all biological material was treated with 0.1% sodium azide (NaN3) solution and stored at 4ºC until analysis.</p>
<p>Metagenome samples:<br />
Two liters of seawater were taken directly from Niskin bottles and filtered onto 47 mm diameter 0.22 µm size pore polycarbonate filters (Millipore) and flash frozen in liquid nitrogen for storage until later analysis. DNA was extracted using the DNeasy Plant Mini Kit from QIAGEN. Illumina adapters and primers for sequencing on PCR products were used (TruSeq). 100 bp, PE reads were generated on the Illumina HiSeq 2500 platform.</p>
<p>Metatranscriptome samples:<br />
Two liters of seawater were taken directly from Niskin bottles and filtered onto 47 mm diameter 0.22 µm size pore polycarbonate filters (Millipore) and flash frozen in liquid nitrogen for storage until later analysis. Illumina ScripSeq kit was used for library prep and ribosomal depletion was done with Epidemiology kit.</p>
<p>Sorted cells metagenome samples:<br />
Size and fluorescene sorted cells (2,000) were resuspended in PBS. Genome amplification was conducted with RepliG kit. Library preparation was conducted with TruSeq kit.</p>
Funding provided by NSF Division of Polar Programs (NSF PLR) Award Number: PLR-1142049 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1142049
completed
Monica V. Orellana
Institute for Systems Biology
Institute for Systems Biology 401 Terry Avenue North
Seattle
WA
98109
USA
monica.orellana@isbscience.org
pointOfContact
Adrian Lopez Garcia de Lomana
Institute for Systems Biology
(206) 732-1255
401 Terry Ave N
Seattle,
WA
98109
Adrian.Lopezgarciadelomana@systemsbiology.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Illumina HiSeq 2500 platform
Sea-Bird Electronics
WET Labs
General Oceanics
theme
None, User defined
Automated DNA Sequencer
CTD Sea-Bird
Fluorometer
Niskin bottle
Sea-Bird SBE 43 Dissolved Oxygen Sensor
Thermal Cycler
instrument
BCO-DMO Standard Instruments
NBP1302
service
Deployment Activity
Ross 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.
TRacing the fate of Algal Carbon Export in the Ross Sea
https://osprey.bco-dmo.org/project/547771
TRacing the fate of Algal Carbon Export in the Ross Sea
<p>Sinking particles are a major element of the biological pump and they are commonly assigned to two fates: mineralization in the water column and accumulation at the seafloor. However, there is another fate of export hidden within the vertical decline of carbon, the transformation of sinking organic matter to fine suspended and/or dissolved organic fractions. This process has been suggested but has rarely been observed or quantified. As a result, it is presumed that the solubilized fraction is largely mineralized over short time scales. However, global ocean surveys of dissolved organic carbon are demonstrating a significant water column accumulation of organic matter under high productivity environments. This proposal will investigate the transformation of organic particles from sinking to solubilized phases of the export flux in the Ross Sea. The Ross Sea experiences high export particle production, low dissolved organic carbon export with overturning circulation, and the area has a predictable succession of production and export events. In addition, the basin is shallow (< 1000 m) so the products the PIs will target are relatively concentrated. To address the proposed hypothesis, the PIs will use both well-established and novel biochemical and optical measures of export production and its fate. The outcomes of this work will help researchers close the carbon budget in the Ross Sea.</p>
TRACERS
largerWorkCitation
project
eng; USA
biota
oceans
Ross Sea
2016-11-30
Ross Sea
0
BCO-DMO catalogue of parameters from Link to NCBI BioProject on programmed cell death from RVIB Nathaniel B. Palmer NBP1302 in the Ross Sea from February to April 2013 (TRACERS 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
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
https://osprey.bco-dmo.org/dataset/666389/data/download
download
onLine
dataset
<p>Sampling:<br />
Water samples collected during the cruise aboard the research vessel icebreaker (RV/IB) Nathaniel B. Palmer, as part of the&nbsp;TRacing&nbsp;the fate of Algal Carbon Export in the Ross Sea (TRACERS) program included nutrients (nitrate, nitrite, silica, phosphate, DOC, DIC, dC13, ). Samples for biological measurements were collected using a rosette sampler fitted with 20 12 L Niskin bottles (General Oceanics), a conductivity, temperature, and depth (CTD) sensor (Sea-Bird Electronics), an SBE 43 dissolved oxygen sensor, and a fluorometer (WET Labs). All seawater samples were stored immediately within 1 h of collection using HDPE amber bottles and all biological material was treated with 0.1% sodium azide (NaN3) solution and stored at 4ºC until analysis.</p>
<p>Metagenome samples:<br />
Two liters of seawater were taken directly from Niskin bottles and filtered onto 47 mm diameter 0.22 µm size pore polycarbonate filters (Millipore) and flash frozen in liquid nitrogen for storage until later analysis. DNA was extracted using the DNeasy Plant Mini Kit from QIAGEN. Illumina adapters and primers for sequencing on PCR products were used (TruSeq). 100 bp, PE reads were generated on the Illumina HiSeq 2500 platform.</p>
<p>Metatranscriptome samples:<br />
Two liters of seawater were taken directly from Niskin bottles and filtered onto 47 mm diameter 0.22 µm size pore polycarbonate filters (Millipore) and flash frozen in liquid nitrogen for storage until later analysis. Illumina ScripSeq kit was used for library prep and ribosomal depletion was done with Epidemiology kit.</p>
<p>Sorted cells metagenome samples:<br />
Size and fluorescene sorted cells (2,000) were resuspended in PBS. Genome amplification was conducted with RepliG kit. Library preparation was conducted with TruSeq kit.</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
Illumina HiSeq 2500 platform
Illumina HiSeq 2500 platform
PI Supplied Instrument Name: Illumina HiSeq 2500 platform 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.
Sea-Bird Electronics
Sea-Bird Electronics
PI Supplied Instrument Name: Sea-Bird Electronics PI Supplied Instrument Description:To measure conductivity, temperature, and depth. Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
WET Labs
WET Labs
PI Supplied Instrument Name: WET Labs PI Supplied Instrument Description:To measure fluorescence Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
General Oceanics
General Oceanics
PI Supplied Instrument Name: General Oceanics PI Supplied Instrument Description:Used to collect water samples Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
PI Supplied Instrument Name: PI Supplied Instrument Description:To measure dissolved oxygen concentration Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/
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: NBP1302
NBP1302
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel
NBP1302
Dennis Hansell
University of Miami Rosenstiel School of Marine and Atmospheric Science
http://dmoserv3.whoi.edu/data_docs/TRACERS/NBP1302_data_report.pdf
Report describing NBP1302
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel