http://lod.bco-dmo.org/id/dataset/684156
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
2017-03-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project)
2017-03-08
publication
2017-03-08
revision
BCO-DMO Linked Data URI
2017-03-08
creation
http://lod.bco-dmo.org/id/dataset/684156
Erica Goetze
University of Hawaiʻi at Mānoa
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) Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (Plankton Population Genetics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-03-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/684156 [access date]
P. xiphias SRA, accessions, collection info Dataset Description: <p>This dataset includes RADSeq data as well as NCBI Short Read Archive (SRA) BioProject and BioSample accessions and collection metadata from animals collected on Atlantic Meridional Transect 22 (AMT22) in Oct. - Nov. 2012. Field work was conducted on the RRS James Cook cruise JC079. See NCBI GenBank Bioproject PRJNA368728 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA368728]</p>
<p>The sequences are embargoed until 2019-12-01. Please check back after that date.</p>
<p>README for processed data files associated with the article: “Genetic isolation between populations in distinct pelagic habitats of the oceanic copepod Pleuromamma xiphias” – Authors: Lauren Van Woudenberg, Matthew Iacchei, Jonathon Whitney, Katja T. C. A. Peijnenburg, Erica Goetze (2017?). in preparation for submission to Molecular Ecology.<br />
<br />
Data files included in this archive:<br />
(1) Supplementary Table 1. Overview of RADSeq data for all animals included in the study. VanWoudenberg_et_al_PLXI_RADSeq.xlsx<br />
<br />
(2) VCF file used in downstream analyses, including mitochondrial clade 3 animals only. 289 total animals included. M4n3_5X_60%indiv_40%miss_final.vcf.<br />
<br />
(3) VCF file used in downstream analyses, for analyses regarding mitochondrial clades 2 &amp; 3 and SNP clusters 1 &amp; 2. 112 total animals included. MTclades_M4n3_5X_60%indiv_40%miss.vcf<br />
<br />
(4) Summary table and metadata of the sequence files submitted to the NCBI Sequence Read Archive (SRA), with BioProject and BioSample numbers. VanWoudenberg_et_al_2017_SRA_metadata.xlsx</p> Methods and Sampling: <p>Please refer to the paper for methodological details. If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.</p>
<p>From the <a href="http://dmoserv3.whoi.edu/data_docs/Goetze/AMT22_cruise/jc079.pdf" target="_blank">cruise report</a>:<br />
<strong>Sample collection.</strong> Plankton samples were collected with 0.71m diameter bongo nets (200, 333 µm), and with an RMT1 midwater trawl (333 µm) that has a nominal mouth area of 1m2. A total of 50 plankton tows were conducted along the cruise leg (Table 1), with 35 tows conducted using the bongo and 14 samples collected with the RMT net. The bongo tows were oblique tows that sampled from between 211 to 488 m depth and the surface (324m average maximum depth of tow). The bongo samples will be used for quantitative estimates of animal abundance along the cruise leg (target species only, tows conducted with timedepth-recorder and flowmeter). The RMT tows were also oblique tows that sampled between 62 to 216 m depth and the surface (153 m average maximum depth of tow). All tows except one (station 42) were conducted at night, in order to efficiently sample the migratory community.</p>
<p><strong>Sample handling and preservation</strong>. All plankton from the 200 µm mesh bongo net was preserved immediately in 100% ethyl alcohol for use in molecular studies, including DNA sequencing and microsatellite genotyping (and possibly RAD tag sequencing), in addition to estimates of abundance of target species. Plankton material from the 333 µm mesh bongo net and the RMT net was sorted live immediately following collection, and animals were individually identified, and preserved in acetone, RNALater, cryopreserved, and in some cases used for live imaging prior to preservation. These animals will be used for molecular, genomic and transcriptomic analyses. Both RNA/DNA ratios and prosome length - dry weight relationships will be used as measures of animal condition in copepods. In total, over 17,000 animals from 40 target species were individually sorted and preserved for this panel of measurements. Following live sorting and imaging of the 333 µm samples, the remaining plankton was preserved either in 4% buffered formalin or 100% ethyl alcohol for morphological studies.</p>
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
onGoing
Erica Goetze
University of Hawaiʻi at Mānoa
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
bioproject_accession
biosample_accession
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
sample_id
cruise_id
sta
lat_collection
lon_collection
date_collection
sex
mtCOI_Clade
num_Seq_reads_initial
num_Seq_reads_post_cleaning
Illumina HiSeq 2500
theme
None, User defined
sample identification
No BCO-DMO term
platform
instrument
file_name
Cruise identfier
station number
latitude
longitude
date
sex
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
JC079
service
Deployment Activity
Southampton, UK to Punta Arenas, Chile
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
biota
oceans
Southampton, UK to Punta Arenas, Chile
-42.0517
-22.4662
-39.88
39.647
2012-10-16
2012-11-17
Atlantic Ocean, 46 N - 46 S
0
BCO-DMO catalogue of parameters from Population genomics study on the planktonic copepod Pleuromamma xiphias: RADSeq data and metadata (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/699910.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699911.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699912.rdf
Name: library_ID
Units: unitless
Description: <p>NCBI Library identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699913.rdf
Name: title
Units: unitless
Description: <p>NCBI project title</p>
http://lod.bco-dmo.org/id/dataset-parameter/699914.rdf
Name: library_strategy
Units: unitless
Description: <p>NCBI term meaning genomic method used for analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/699915.rdf
Name: library_source
Units: unitless
Description: <p>NCBI term meaning the type of genomic material that was analyzed</p>
http://lod.bco-dmo.org/id/dataset-parameter/699916.rdf
Name: library_selection
Units: unitless
Description: <p>NCBI term meaning method that the source material was selected</p>
http://lod.bco-dmo.org/id/dataset-parameter/699917.rdf
Name: library_layout
Units: unitless
Description: <p>NCBI library layout: Paired-end or Single</p>
http://lod.bco-dmo.org/id/dataset-parameter/699918.rdf
Name: platform
Units: unitless
Description: <p>platform used for sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/699919.rdf
Name: instrument_model
Units: unitless
Description: <p>sequencing instrument model</p>
http://lod.bco-dmo.org/id/dataset-parameter/699920.rdf
Name: design_description
Units: unitless
Description: <p>NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/699921.rdf
Name: filetype
Units: unitless
Description: <p>type of file</p>
http://lod.bco-dmo.org/id/dataset-parameter/699922.rdf
Name: filename
Units: unitless
Description: <p>file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/699923.rdf
Name: sample_id
Units: unitless
Description: <p>sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699924.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/699925.rdf
Name: sta
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/699926.rdf
Name: lat_collection
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/699927.rdf
Name: lon_collection
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/699928.rdf
Name: date_collection
Units: unitless
Description: <p>collection date formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/699929.rdf
Name: sex
Units: unitless
Description: <p>sex of specimens</p>
http://lod.bco-dmo.org/id/dataset-parameter/699930.rdf
Name: mtCOI_Clade
Units: unitless
Description: <p>mitochondrial COI clade</p>
http://lod.bco-dmo.org/id/dataset-parameter/699931.rdf
Name: num_Seq_reads_initial
Units: reads
Description: <p>number of sequence reads pre-cleaning</p>
http://lod.bco-dmo.org/id/dataset-parameter/699932.rdf
Name: num_Seq_reads_post_cleaning
Units: reads
Description: <p>number of sequence reads post-cleaning</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
https://osprey.bco-dmo.org/dataset/684156/data/download
download
onLine
dataset
<p>Please refer to the paper for methodological details. If you have further questions, please contact the corresponding author (Dr. Erica Goetze): egoetze[at]hawaii[dot]edu.</p>
<p>From the <a href="http://dmoserv3.whoi.edu/data_docs/Goetze/AMT22_cruise/jc079.pdf" target="_blank">cruise report</a>:<br />
<strong>Sample collection.</strong> Plankton samples were collected with 0.71m diameter bongo nets (200, 333 µm), and with an RMT1 midwater trawl (333 µm) that has a nominal mouth area of 1m2. A total of 50 plankton tows were conducted along the cruise leg (Table 1), with 35 tows conducted using the bongo and 14 samples collected with the RMT net. The bongo tows were oblique tows that sampled from between 211 to 488 m depth and the surface (324m average maximum depth of tow). The bongo samples will be used for quantitative estimates of animal abundance along the cruise leg (target species only, tows conducted with timedepth-recorder and flowmeter). The RMT tows were also oblique tows that sampled between 62 to 216 m depth and the surface (153 m average maximum depth of tow). All tows except one (station 42) were conducted at night, in order to efficiently sample the migratory community.</p>
<p><strong>Sample handling and preservation</strong>. All plankton from the 200 µm mesh bongo net was preserved immediately in 100% ethyl alcohol for use in molecular studies, including DNA sequencing and microsatellite genotyping (and possibly RAD tag sequencing), in addition to estimates of abundance of target species. Plankton material from the 333 µm mesh bongo net and the RMT net was sorted live immediately following collection, and animals were individually identified, and preserved in acetone, RNALater, cryopreserved, and in some cases used for live imaging prior to preservation. These animals will be used for molecular, genomic and transcriptomic analyses. Both RNA/DNA ratios and prosome length - dry weight relationships will be used as measures of animal condition in copepods. In total, over 17,000 animals from 40 target species were individually sorted and preserved for this panel of measurements. Following live sorting and imaging of the 333 µm samples, the remaining plankton was preserved either in 4% buffered formalin or 100% ethyl alcohol for morphological studies.</p>
Specified by the Principal Investigator(s)
<p>SEQUENCE DATA FILES<br />
Illumina HiSeq reads are available NCBI Sequence Read Archive (SRA). Libraries were prepared following the ezRAD protocol (Toonen et al. 2013). Sequences from Illumina HiSeq 2500, with quality trimming and adaptor removal using TrimGalore (as follows).<br />
<br />
#ADAPTERS<br />
#Illumina TruSeq HT dual-indexed Adapters (96 barcode combinations)<br />
GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG #Read1 w/ 8 digit wildcard i7 #barcode<br />
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTNNNNNNNNGTGTAGATCTCGGTGGTCGCCGTATCATT&nbsp; #Read2 w/ wildcard i5 barcode (reverse complemented)<br />
<br />
#TrimGalore Command<br />
#first make directory for cleaned files<br />
mkdir&nbsp;cleaned_for_stacks<br />
<br />
##FOR R1 loop for trim_galore##<br />
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)<br />
<br />
for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcacacgtctgaactccagtcacnnnnnnnnatctcgtatgccgtcttctgcttg --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R1.fq; done<br />
<br />
##FOR R2 loop for trim_galore##<br />
declare -a TEST=(site09_12 site09_15 site09_18 site09_21 site09_24 site09_13 site09_16 site09_19 site09_22 site09_14 site09_17 site09_20 site09_23)<br />
<br />
for i in "${TEST[@]}"; do perl ~/ddocent/trim_galore —-phred33 —-dont_gzip -a gatcggaagagcgtcgtgtagggaaagagtgtnnnnnnnngtgtagatctcggtggtcgccgtatcatt --stringency 5 -e 0.1 -r1 100 --output_dir ./cleaned_for_stacks $i.R2.fq; done<br />
<br />
Contact: Erica Goetze for any questions, or for subsequent use of these data.</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 />
combined SRA metadata with collection information<br />
converted latitude and longitude to decimal degrees<br />
added links to NCBI GenBank BioProject and BioSample pages</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
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 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: 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: JC079
JC079
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel
JC079
Glen Tarran
Plymouth Marine Laboratory
http://dmoserv3.whoi.edu/data_docs/Goetze/AMT22_cruise/jc079.pdf
Report describing JC079
RRS James Cook
Community Standard Description
International Council for the Exploration of the Sea
RRS James Cook
vessel