http://lod.bco-dmo.org/id/dataset/700961
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
2017-05-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project)
2017-05-25
publication
2017-05-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2017-06-12
publication
https://doi.org/10.1575/1912/bco-dmo.704665
Dr Erica Goetze
University of Hawaii
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: Goetze, Erica (2017) NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Dataset version 2017-05-25 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.704665 [access date]
NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample Dataset Description: <p>These data include sample information and accession links to sequence data at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).</p><p>This data submission consists of metabarcoding data for the zooplankton community in the epipelagic, mesopelagic and upper bathypelagic zones (0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to assess the hidden diversity present in zooplankton assemblages in midwaters, and detect vertical gradients in species richness, depth distributions, and community composition of the full zooplankton assemblage. Samples were collected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS, 200um mesh), on R/V Falkor cruise FK140613. &nbsp;Next generation sequence data (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton assemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers described in Fonseca et al. 2010). The data includes sequences and read count abundance information for molecular OTUs from both holoplanktonic and meroplanktonic taxa</p><p>Related dataset containing OTU tables and fasta sequences (representative / most abundance read for each OTU):<br /><a href="http://www.bco-dmo.org/dataset/700279">Metabarcoding zooplankton at </a><a href="http://www.bco-dmo.org/dataset/700279">station</a><a href="http://www.bco-dmo.org/dataset/700279"> ALOHA: OTU tables and </a><a href="http://www.bco-dmo.org/dataset/700279">fasta</a><a href="http://www.bco-dmo.org/dataset/700279"> files</a></p> Acquisition Description: <p><strong>SAMPLE INFORMATION</strong></p><p>Sample identifiers include the following codes.</p><p><strong>MOCNESS tow</strong><br />FA3: Night sampling<br />FA4: Day sampling</p><p><strong>Depth range:</strong><br />N1: 1500-1000m<br />N2: 1000-700m<br />N3: 700-500m<br />N4: 500-300m<br />N5: 300-200m<br />N6: 200-150m<br />N7: 150-100m<br />N8: 100-50m<br />N9: 50m-0m</p><p><strong>Wet-sieved zooplankton size fractions</strong><br />SF1: 0.2-0.5 mm<br />SF2: 0.5-1.0 mm<br />SF3: 1.0-2.0 mm</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1255697
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1338959 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1338959
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029478 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1029478
completed
Dr Erica Goetze
University of Hawaii
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
asNeeded
Unknown
analysis_name
lat
lon
library_ID
bioproject_accession
biosample_accession
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
Illumina MiSeq
quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)
Agilent 2100 Bioanalyzer
theme
None, User defined
sample description
latitude
longitude
sample identification
accession number
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
PCR Thermal Cycler
Bioanalyzer
instrument
BCO-DMO Standard Instruments
FK140613
service
Deployment Activity
Station ALOHA
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.
Basin-scale genetics of marine zooplankton
http://www.bco-dmo.org/project/537991
Basin-scale genetics of marine zooplankton
Description from NSF award abstract:Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).Online science outreach blog at: https://atlanticplankton.wordpress.com
Plankton Population Genetics
largerWorkCitation
project
eng; USA
oceans
Station ALOHA
-158
-158
22.75
22.75
2014-06-13
2014-06-19
Atlantic Ocean, 46 N - 46 S
0
BCO-DMO catalogue of parameters from NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics 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/704503.rdf
Name: analysis_name
Units: unitless
Description: Descriptive name of analysis including percent clustering and subsampling or no subsampling
http://lod.bco-dmo.org/id/dataset-parameter/704504.rdf
Name: lat
Units: decimal degrees
Description: Latitude of sample site (Station ALOHA)
http://lod.bco-dmo.org/id/dataset-parameter/704505.rdf
Name: lon
Units: decimal degrees
Description: Longitude of sample site (Station ALOHA)
http://lod.bco-dmo.org/id/dataset-parameter/704506.rdf
Name: library_ID
Units: unitless
Description: Short unique identifier for the sequencing library.
http://lod.bco-dmo.org/id/dataset-parameter/704507.rdf
Name: bioproject_accession
Units: unitless
Description: NCBI BioProject identifier
http://lod.bco-dmo.org/id/dataset-parameter/704508.rdf
Name: biosample_accession
Units: unitless
Description: NCBI BioSample identifier
http://lod.bco-dmo.org/id/dataset-parameter/704509.rdf
Name: title
Units: unitless
Description: Short description that will identify the dataset on public pages.
http://lod.bco-dmo.org/id/dataset-parameter/704510.rdf
Name: library_strategy
Units: unitless
Description: Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products
http://lod.bco-dmo.org/id/dataset-parameter/704511.rdf
Name: library_source
Units: unitless
Description: Metagenomic = Mixed material from metagenome
http://lod.bco-dmo.org/id/dataset-parameter/704512.rdf
Name: library_selection
Units: unitless
Description: PCR = Source material was selected by designed primers
http://lod.bco-dmo.org/id/dataset-parameter/704513.rdf
Name: library_layout
Units: unitless
Description: Paired-end or Single
http://lod.bco-dmo.org/id/dataset-parameter/704514.rdf
Name: platform
Units: unitless
Description: Sequencing platforms [Illumina]
http://lod.bco-dmo.org/id/dataset-parameter/704515.rdf
Name: instrument_model
Units: unitless
Description: Illumina instrument and model used for sequencing
http://lod.bco-dmo.org/id/dataset-parameter/704516.rdf
Name: design_description
Units: unitless
Description: Free-form description of the methods used to create the sequencing library; a brief materials and methods section.
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
http://vocab.nerc.ac.uk/collection/P09/current/LATX/
Name: LATITUDE
Description: The angular distance north or south from the equator, measured along the meridian of the point of interest.
http://vocab.nerc.ac.uk/collection/P09/current/LONX/
Name: LONGITUDE
Description: The angular distance east or west east or west of Greenwich to the point of interest.
http://vocab.nerc.ac.uk/collection/P02/current/ACYC/
Name: Reference numbers
Description: Data record, event, sample or measurement reference numbers
Parameters for this dataset
physicalMeasurement
analysis_name
sample description
PI-supplied Description: Descriptive name of analysis including percent clustering and subsampling or no subsampling; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704503.rdf
unitless
lat
latitude
PI-supplied Description: Latitude of sample site (Station ALOHA); General Description: latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes NERC Description: The angular distance north or south from the equator, measured along the meridian of the point of interest.
http://lod.bco-dmo.org/id/dataset-parameter/704504.rdf
decimal degrees
lon
longitude
PI-supplied Description: Longitude of sample site (Station ALOHA); General Description: longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes NERC Description: The angular distance east or west east or west of Greenwich to the point of interest.
http://lod.bco-dmo.org/id/dataset-parameter/704505.rdf
decimal degrees
library_ID
sample identification
PI-supplied Description: Short unique identifier for the sequencing library.; General Description: unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent NERC Description: Data record, event, sample or measurement reference numbers
http://lod.bco-dmo.org/id/dataset-parameter/704506.rdf
unitless
bioproject_accession
accession number
PI-supplied Description: NCBI BioProject identifier; General Description: Database identifier assigned by repository and linked to GenBank or other repository.
http://lod.bco-dmo.org/id/dataset-parameter/704507.rdf
unitless
biosample_accession
accession number
PI-supplied Description: NCBI BioSample identifier; General Description: Database identifier assigned by repository and linked to GenBank or other repository.
http://lod.bco-dmo.org/id/dataset-parameter/704508.rdf
unitless
title
sample description
PI-supplied Description: Short description that will identify the dataset on public pages.; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704509.rdf
unitless
library_strategy
sample description
PI-supplied Description: Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704510.rdf
unitless
library_source
sample description
PI-supplied Description: Metagenomic = Mixed material from metagenome; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704511.rdf
unitless
library_selection
sample description
PI-supplied Description: PCR = Source material was selected by designed primers; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704512.rdf
unitless
library_layout
sample description
PI-supplied Description: Paired-end or Single; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704513.rdf
unitless
platform
sample description
PI-supplied Description: Sequencing platforms [Illumina]; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704514.rdf
unitless
instrument_model
instrument
PI-supplied Description: Illumina instrument and model used for sequencing; General Description: instrument used to collect or process data, definition is specific to the data set in which it appears
http://lod.bco-dmo.org/id/dataset-parameter/704515.rdf
unitless
design_description
sample description
PI-supplied Description: Free-form description of the methods used to create the sequencing library; a brief materials and methods section.; General Description: text description of sample collected
http://lod.bco-dmo.org/id/dataset-parameter/704516.rdf
unitless
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://doi.org/10.1575/1912/bco-dmo.704665
download
onLine
dataset
<p><strong>SAMPLE INFORMATION</strong></p><p>Sample identifiers include the following codes.</p><p><strong>MOCNESS tow</strong><br />FA3: Night sampling<br />FA4: Day sampling</p><p><strong>Depth range:</strong><br />N1: 1500-1000m<br />N2: 1000-700m<br />N3: 700-500m<br />N4: 500-300m<br />N5: 300-200m<br />N6: 200-150m<br />N7: 150-100m<br />N8: 100-50m<br />N9: 50m-0m</p><p><strong>Wet-sieved zooplankton size fractions</strong><br />SF1: 0.2-0.5 mm<br />SF2: 0.5-1.0 mm<br />SF3: 1.0-2.0 mm</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO processing notes:<br />* commas in the data were replaced with semicolons to support export as csv format.</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 MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Illumina MiSeq using V3 chemistry (300-bp, paired-end) Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument 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.
quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)
quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)
PI Supplied Instrument Name: quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology) Instrument Name: PCR Thermal Cycler Instrument Short Name:Thermal Cycler Instrument 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)
Agilent 2100 Bioanalyzer
Agilent 2100 Bioanalyzer
PI Supplied Instrument Name: Agilent 2100 Bioanalyzer 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.
Cruise: FK140613
FK140613
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK140613
Dr Erica Goetze
University of Hawaii
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel