http://lod.bco-dmo.org/id/dataset/700279
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
2017-05-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (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.704664
Erica Goetze
University of Hawai'i
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, E. (2017) Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (Plankton Population Genetics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-05-25 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.700279.1 [access date]
Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU Dataset Description: <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&nbsp;Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS, 200um mesh), on R/V Falkor cruise FK140613. 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.&nbsp;&nbsp;All results derive from analyses in&nbsp;mothur&nbsp;v1.36.1 (Schloss et al. 2009, Kozich et al. 2013).<strong> </strong></p>
<p>Tables from four analyses are included in this submission:</p>
<p>1) 97_OTUtable:&nbsp;read counts for each OTU (clustered at 97% similarity) across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.&nbsp;</p>
<p>2) 97_OTU_subsampled: read counts for each OTU (clustered at 97% similarity), subsampled for even sequencing coverage across 54 samples (depth, size fractionated, with NCBI BLAST results for the top representative sequence from each OTU.</p>
<p>3) 99_OTU: read counts for each OTU (clustered at 99% similarity) across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.&nbsp;</p>
<p>4) 99_OTU_subsampled: read counts for each OTU (clustered at 99% similarity), subsampled for even sequencing coverage across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.</p>
<p>Related dataset containing NCBI accession numbers for sequence data:<br />
Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers&nbsp;www.bco-dmo.org/dataset/700961</p> Methods and Sampling: <p><strong>Sample Codes:</strong></p>
<p>Read count parameter names (e.g. FA3_N7_SF1) include the following three 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>
<p>Data parameters with the prefix (NCBI_) are from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/)</p>
<p>Data parameters with the prefix (silva_) are from the Silva database (https://www.arb-silva.de/).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1255697
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1338959 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1338959
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029478 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029478
completed
Erica Goetze
University of Hawai'i
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
analysis_name
lat
lon
OTU_ID
FA3_N1_SF1
FA3_N1_SF2
FA3_N1_SF3
FA3_N2_SF1
FA3_N2_SF2
FA3_N2_SF3
FA3_N3_SF1
FA3_N3_SF2
FA3_N3_SF3
FA3_N4_SF1
FA3_N4_SF2
FA3_N4_SF3
FA3_N5_SF1
FA3_N5_SF2
FA3_N5_SF3
FA3_N6_SF1
FA3_N6_SF2
FA3_N6_SF3
FA3_N7_SF1
FA3_N7_SF2
FA3_N7_SF3
FA3_N8_SF1
FA3_N8_SF2
FA3_N8_SF3
FA3_N9_SF1
FA3_N9_SF2
FA3_N9_SF3
FA4_N1_SF1
FA4_N1_SF2
FA4_N1_SF3
FA4_N2_SF1
FA4_N2_SF2
FA4_N2_SF3
FA4_N3_SF1
FA4_N3_SF2
FA4_N3_SF3
FA4_N4_SF1
FA4_N4_SF2
FA4_N4_SF3
FA4_N5_SF1
FA4_N5_SF2
FA4_N5_SF3
FA4_N6_SF1
FA4_N6_SF2
FA4_N6_SF3
FA4_N7_SF1
FA4_N7_SF2
FA4_N7_SF3
FA4_N8_SF1
FA4_N8_SF2
FA4_N8_SF3
FA4_N9_SF1
FA4_N9_SF2
FA4_N9_SF3
silva_tax_level1
silva_tax_level2
silva_tax_level3
silva_tax_level4
silva_tax_level5
silva_tax_level6
silva_tax_level7
silva_tax_level8
silva_tax_level9
silva_tax_level10
silva_tax_level11
silva_tax_level12
silva_tax_level13
silva_tax_level14
assigned_habitat
NCBI_query_sequence_id
NCBI_top_hit
NCBI_percent_identity
NCBI_percent_coverage
NCBI_sequence_length
NCBI_mismatch
NCBI_evalue
NCBI_bitscore
NCBI_percent_positive
NCBI_top_hit_taxID
NCBI_top_hit_title
analysis_description
Illumina MiSeq
Agilent 2100 Bioanalyzer
quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)
theme
None, User defined
sample description
latitude
longitude
sample identification
count
taxon
sequence
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bioanalyzer
Thermal Cycler
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
https://osprey.bco-dmo.org/project/537991
Basin-scale genetics of marine zooplankton
<p><em>Description from NSF award abstract:</em><br />
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.</p>
<p>Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the <a href="http://dmoserv3.whoi.edu/data_docs/Goetze/AMT24_cruise/GOETZE_AMT24_Cruise_Report.pdf" target="_blank">AMT24 zooplankton ecology cruise report (PDF)</a>.</p>
<p>Online science outreach blog at: <a href="https://atlanticplankton.wordpress.com" target="_blank">https://atlanticplankton.wordpress.com</a></p>
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 Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (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/704533.rdf
Name: analysis_name
Units: unitless
Description: <p>Descriptive name of analysis including percent clustering and subsampling or no subsampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/704534.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample site (Station ALOHA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704535.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample site (Station ALOHA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704536.rdf
Name: OTU_ID
Units: unitless
Description: <p>Operational taxonomic unit (OTU) identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/704537.rdf
Name: FA3_N1_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704538.rdf
Name: FA3_N1_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704539.rdf
Name: FA3_N1_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704540.rdf
Name: FA3_N2_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704541.rdf
Name: FA3_N2_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704542.rdf
Name: FA3_N2_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704543.rdf
Name: FA3_N3_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704544.rdf
Name: FA3_N3_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704545.rdf
Name: FA3_N3_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704546.rdf
Name: FA3_N4_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704547.rdf
Name: FA3_N4_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704548.rdf
Name: FA3_N4_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704549.rdf
Name: FA3_N5_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704550.rdf
Name: FA3_N5_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704551.rdf
Name: FA3_N5_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704552.rdf
Name: FA3_N6_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704553.rdf
Name: FA3_N6_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704554.rdf
Name: FA3_N6_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704555.rdf
Name: FA3_N7_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704556.rdf
Name: FA3_N7_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704557.rdf
Name: FA3_N7_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704558.rdf
Name: FA3_N8_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704559.rdf
Name: FA3_N8_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704560.rdf
Name: FA3_N8_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704561.rdf
Name: FA3_N9_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704562.rdf
Name: FA3_N9_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704563.rdf
Name: FA3_N9_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704564.rdf
Name: FA4_N1_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704565.rdf
Name: FA4_N1_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704566.rdf
Name: FA4_N1_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704567.rdf
Name: FA4_N2_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704568.rdf
Name: FA4_N2_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704569.rdf
Name: FA4_N2_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704570.rdf
Name: FA4_N3_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704571.rdf
Name: FA4_N3_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704572.rdf
Name: FA4_N3_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704573.rdf
Name: FA4_N4_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704574.rdf
Name: FA4_N4_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704575.rdf
Name: FA4_N4_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704576.rdf
Name: FA4_N5_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704577.rdf
Name: FA4_N5_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704578.rdf
Name: FA4_N5_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704579.rdf
Name: FA4_N6_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704580.rdf
Name: FA4_N6_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704581.rdf
Name: FA4_N6_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704582.rdf
Name: FA4_N7_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704583.rdf
Name: FA4_N7_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704584.rdf
Name: FA4_N7_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704585.rdf
Name: FA4_N8_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704586.rdf
Name: FA4_N8_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704587.rdf
Name: FA4_N8_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704588.rdf
Name: FA4_N9_SF1
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 1 (0.2 - 0.5mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704589.rdf
Name: FA4_N9_SF2
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 2 (0.5 - 0.1mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704590.rdf
Name: FA4_N9_SF3
Units: per OTU
Description: <p>Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 3 (1.0 - 2.0 mm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704591.rdf
Name: silva_tax_level1
Units: unitless
Description: <p>Taxonomic classification level 1 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704592.rdf
Name: silva_tax_level2
Units: unitless
Description: <p>Taxonomic classification level 2 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704593.rdf
Name: silva_tax_level3
Units: unitless
Description: <p>Taxonomic classification level 3 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704594.rdf
Name: silva_tax_level4
Units: unitless
Description: <p>Taxonomic classification level 4 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704595.rdf
Name: silva_tax_level5
Units: unitless
Description: <p>Taxonomic classification level 5 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704596.rdf
Name: silva_tax_level6
Units: unitless
Description: <p>Taxonomic classification level 6 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704597.rdf
Name: silva_tax_level7
Units: unitless
Description: <p>Taxonomic classification level 7 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704598.rdf
Name: silva_tax_level8
Units: unitless
Description: <p>Taxonomic classification level 8 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704599.rdf
Name: silva_tax_level9
Units: unitless
Description: <p>Taxonomic classification level 9 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704600.rdf
Name: silva_tax_level10
Units: unitless
Description: <p>Taxonomic classification level 10 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704601.rdf
Name: silva_tax_level11
Units: unitless
Description: <p>Taxonomic classification level 11 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704602.rdf
Name: silva_tax_level12
Units: unitless
Description: <p>Taxonomic classification level 12 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704603.rdf
Name: silva_tax_level13
Units: unitless
Description: <p>Taxonomic classification level 13 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704604.rdf
Name: silva_tax_level14
Units: unitless
Description: <p>Taxonomic classification level 14 for each OTU; assigned by mothur based on the Silva database</p>
http://lod.bco-dmo.org/id/dataset-parameter/704605.rdf
Name: assigned_habitat
Units: unitless
Description: <p>Assigned community/habitat, based on both mothur classification and NCBI top hit</p>
http://lod.bco-dmo.org/id/dataset-parameter/704606.rdf
Name: NCBI_query_sequence_id
Units: unitless
Description: <p>Query sequence (BLAST qseqid); header description of representative sequence from fasta file</p>
http://lod.bco-dmo.org/id/dataset-parameter/704607.rdf
Name: NCBI_top_hit
Units: unitless
Description: <p>Subject sequence id (BLAST sseqid): sequence identifier for subject sequence from NCBI; Contains two NCBI accession numbers</p>
http://lod.bco-dmo.org/id/dataset-parameter/704608.rdf
Name: NCBI_percent_identity
Units: unitless
Description: <p>Percent identity (BLAST pident): percentage of identical matches in the alignment</p>
http://lod.bco-dmo.org/id/dataset-parameter/704609.rdf
Name: NCBI_percent_coverage
Units: unitless
Description: <p>Percent coverage (BLAST qcovs): query coverage per sequence for all high-scoring segment pairs (HSPs)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704610.rdf
Name: NCBI_sequence_length
Units: unitless
Description: <p>Alignment length (BLAST length)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704611.rdf
Name: NCBI_mismatch
Units: unitless
Description: <p>Number of mismatches (BLAST mismatch)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704612.rdf
Name: NCBI_evalue
Units: unitless
Description: <p>Expectation value of match (BLAST evalue)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704613.rdf
Name: NCBI_bitscore
Units: unitless
Description: <p>Normalized alignment score for comparison across searches (BLAST bitscore)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704614.rdf
Name: NCBI_percent_positive
Units: unitless
Description: <p>Percentage of positive-scoring matches (BLAST ppos)</p>
http://lod.bco-dmo.org/id/dataset-parameter/704615.rdf
Name: NCBI_top_hit_taxID
Units: unitless
Description: <p>Taxonomic identifiers (BLAST staxids): unique subject taxonomy ID(s); multiple IDs are separated by a semicolon</p>
http://lod.bco-dmo.org/id/dataset-parameter/704616.rdf
Name: NCBI_top_hit_title
Units: unitless
Description: <p>Subject title from NCBI entry (BLAST stitle)</p>
http://lod.bco-dmo.org/id/dataset-parameter/792797.rdf
Name: analysis_description
Units: unitless
Description: <p>Analysis description</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
2114513
https://darchive.mblwhoilibrary.org/bitstream/1912/25410/1/RepSeqs99.fasta
download
2147766
https://darchive.mblwhoilibrary.org/bitstream/1912/25410/2/RepSeqs97.fasta
download
12157238
https://darchive.mblwhoilibrary.org/bitstream/1912/25410/3/dataset-700279_metabarcoding-zooplankton-station-aloha-otu-tables-and-fasta-files__v1.tsv
download
8876538
https://darchive.mblwhoilibrary.org/bitstream/1912/9039/6/data_OTU_700279_2017-05-25.tsv
download
https://doi.org/10.1575/1912/bco-dmo.704664
download
onLine
dataset
<p><strong>Sample Codes:</strong></p>
<p>Read count parameter names (e.g. FA3_N7_SF1) include the following three 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>
<p>Data parameters with the prefix (NCBI_) are from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/)</p>
<p>Data parameters with the prefix (silva_) are from the Silva database (https://www.arb-silva.de/).</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&nbsp;csv&nbsp;format.<br />
* fasta files added to dataset</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: 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 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.
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: 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: FK140613
FK140613
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK140613
Erica Goetze
University of Hawai'i
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel