http://lod.bco-dmo.org/id/dataset/940678
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
2024-10-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020
2024-10-21
publication
2024-10-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-10-22
publication
https://doi.org/10.26008/1912/bco-dmo.940678.1
Michael J. Metzger
Pacific Northwest Research Institute
principalInvestigator
Ryan Crim
Puget Sound Restoration Fund
principalInvestigator
Elizabeth Unsell
Suquamish Tribe
principalInvestigator
Cathryn Abbott
Fisheries and Oceans Canada, Pacific Region
principalInvestigator
James Dimond
Western Washington University
principalInvestigator
Helen Gurney-Smith
Fisheries and Oceans Canada, Pacific Region
principalInvestigator
Robin Little Wing Sigo
Suquamish Tribe
principalInvestigator
Peter Smith
Pacific Northwest Research Institute
principalInvestigator
Janine Supernault
Fisheries and Oceans Canada, Pacific Region
principalInvestigator
Lauren Vandepas
University of Miami
principalInvestigator
Sydney Weinandt
Pacific Northwest Research Institute
principalInvestigator
Ruth Withler
Fisheries and Oceans Canada, Pacific Region
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: Yonemitsu, M., Sevigny, J., Vandepas, L., Dimond, J., Giersch, R., Gurney-Smith, H., Abbott, C., Supernault, J., Withler, R., Smith, P., Weinandt, S., Garrett, F., Child, Z., Little Wing Sigo, R., Unsell, E., Crim, R., Metzger, M. J. (2024) Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.940678.1 [access date]
Methods and Sampling: <p>Microsatellites were amplified from DNA extracted from both hemocyte and tissue using Taq polymerase (Genesee Scientific) for a select number of basket cockles (Clinocardium nuttallii, urn:lsid:marinespecies.org:taxname:381980) colelcted from multipl intertidal locations in Washington State, USA. All possible neoplastic animals based on positive qPCR screen (n=26) and one randomly selected, non-neoplastic animal from each collection (n=12) were selected for microsatellite amplification and fragment analysis. Microsatellites were amplified using primers for 8 polymorphic loci: Cnu48, Cnu55, Cnu58, Cnu63, Cnu68, Cnu72, Cnu78, and Cnu81.&nbsp;<br />
<br />
Instrument Description:&nbsp;Allele sizes were identified by fragment analysis using fluorescent primers (6-FAM, PET, NED, and VIC) and a 3730xl Genetic Analyzer with the LIZ-500 size standard.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2208081 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2208081
completed
Michael J. Metzger
Pacific Northwest Research Institute
720 Broadway
Seattle
WA
98122-4327
USA
metzgerm@pnri.org
pointOfContact
Ryan Crim
Puget Sound Restoration Fund
ryan@restorationfund.org
pointOfContact
Elizabeth Unsell
Suquamish Tribe
eunsell@suquamish.nsn.us
pointOfContact
Cathryn Abbott
Fisheries and Oceans Canada, Pacific Region
cathryn.abbott@dfo-mpo.gc.ca
pointOfContact
James Dimond
Western Washington University
dimondj2@wwu.edu
pointOfContact
Helen Gurney-Smith
Fisheries and Oceans Canada, Pacific Region
helen.gurney-smith@dfo-mpo.gc.ca
pointOfContact
Robin Little Wing Sigo
Suquamish Tribe
rsigo@suquamish.nsn.us
pointOfContact
Peter Smith
Pacific Northwest Research Institute
psmith@pnri.org
pointOfContact
Janine Supernault
Fisheries and Oceans Canada, Pacific Region
janine.supernault@dfo-mpo.gc.ca
pointOfContact
Lauren Vandepas
University of Miami
vandepaslauren@gmail.com
pointOfContact
Sydney Weinandt
Pacific Northwest Research Institute
sweinandt@pnri.org
pointOfContact
Ruth Withler
Fisheries and Oceans Canada, Pacific Region
ruth.withler@dfo-mpo.gc.ca
pointOfContact
asNeeded
Dataset Version: 1
Unknown
filename
filesize_bytes
md5sum
site_code
Location
Beach_Name
Collection_Date
Tribe_Agency
GPS_Lat
GPS_Lon
Time
Tidal_Height
Collection_DateTime_UTC
3730xl Genetic Analyzer with the LIZ-500 size standard
theme
None, User defined
file_name
No BCO-DMO term
site
site description
date_local
latitude
longitude
time_local
tide
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
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.
Quantifying and modeling the transmission dynamics of bivalve transmissible neoplasia
https://osprey.bco-dmo.org/project/936145
Quantifying and modeling the transmission dynamics of bivalve transmissible neoplasia
<p><em>NSF Award Abstract:</em><br />
Cancer is not normally thought of as an infectious disease. However, several transmissible cancers have recently been found in the wild, in which the cancer cells themselves jump from animal to animal as an infectious agent, causing significant mortality on land and in the marine environment. Marine bivalves appear to be particularly susceptible. At least nine lineages of lethal transmissible cancer have been identified in eight bivalve species worldwide since they were first recognized as an infectious cancer by members of this team less than a decade ago. It is known that whole cancer cells transfer from one animal to another, but it is unclear how this infectious disease spreads at the individual level, within a single population, or between populations in the environment. The interdisciplinary team is combining sensitive field surveys of disease prevalence, laboratory inoculation, and in vitro experiments together with quantitative modeling to understand how this unique class of infectious disease spreads in nature. The team will continue to communicate the results of this project through scientific publications and meetings with commercial aquaculture and local Native American communities, including research partners in multiple Coast Salish Tribes. Understanding the disease transmission principles may help develop strategies to control this disease, which would directly help these communities. The team members are also training undergraduate students during summer research experiences at Pacific Northwest Research Institute, Western Washington University, and Bigelow Laboratory for Ocean Sciences.</p>
<p>To understand the basic principles of the spread of bivalve transmissible cancer, the team studies two separate lineages in geographically separated species: soft-shell clams (Mya arenaria) on the Atlantic Coast of North America, the first bivalve transmissible cancer identified; and basket cockles (Clinocardium nuttallii), a species on the Pacific Coast of North America, in which the team has just recently identified bivalve transmissible cancer. The team is developing two quantitative models, one for the spread of disease within a population over time, and a second to model the spread of cancer lineages between different populations. They are testing these models with regular disease prevalence data from wild populations from multiple sites. Laboratory work on disease progression and transmission supports development and refinement of these models by providing critical parameter values and testing whether environmental variables (such as temperature) or genetic variables (such as the relatedness of cancer and host) affect the susceptibility and timing of disease progression. This project aims to develop a quantitative understanding of disease dynamics in soft-shell clams and basket cockles. Ultimately, it will provide general principles that underlie the spread of this recently discovered class of infectious disease.</p>
<p>This project was funded by the Division of Environmental Biology and the Division of Ocean Sciences.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Transmission of BTN
largerWorkCitation
project
eng; USA
oceans
-124.62356
-122.5539
46.68
48.983317
2019-03-18
2020-01-09
East and West coasts of USA
0
BCO-DMO catalogue of parameters from Fragment analysis files from microsatellite analysis of samples of the basket cockle (Clinocardium nuttallii) from multiple sites in Washington State between Mar of 2019 and Jan of 2020
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/940915.rdf
Name: filename
Units: unitless
Description: <p>Filename of the .fsa file (included in All_Cnu_microsatellites_combined.zip)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940916.rdf
Name: filesize_bytes
Units: bytes
Description: <p>filesize in bytes</p>
http://lod.bco-dmo.org/id/dataset-parameter/940917.rdf
Name: md5sum
Units: unitless
Description: <p>checksum (md5 hash) which can be used to verify intergrity of transferred files.</p>
http://lod.bco-dmo.org/id/dataset-parameter/940918.rdf
Name: site_code
Units: unitless
Description: <p>Site Code</p>
http://lod.bco-dmo.org/id/dataset-parameter/940919.rdf
Name: Location
Units: unitless
Description: <p>Site location description</p>
http://lod.bco-dmo.org/id/dataset-parameter/940920.rdf
Name: Beach_Name
Units: unitless
Description: <p>Beach name (e.g. "Front Beach")</p>
http://lod.bco-dmo.org/id/dataset-parameter/940921.rdf
Name: Collection_Date
Units: unitless
Description: <p>Collection date (local time zone PST/PDT)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940922.rdf
Name: Tribe_Agency
Units: unitless
Description: <p>Tribal Agency</p>
http://lod.bco-dmo.org/id/dataset-parameter/940923.rdf
Name: GPS_Lat
Units: decimal degrees
Description: <p>Site latitude for collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940924.rdf
Name: GPS_Lon
Units: decimal degrees
Description: <p>Site longitude for collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940925.rdf
Name: Time
Units: unitless
Description: <p>Collection time (local time zone PST/PDT)</p>
http://lod.bco-dmo.org/id/dataset-parameter/940926.rdf
Name: Tidal_Height
Units: feet (ft)
Description: <p>Tidal height at time of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/940927.rdf
Name: Collection_DateTime_UTC
Units: unitless
Description: <p>Datetime with timezone for collection (UTC)</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
27639843
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/0f60be61-81ea-4aa1-ab5f-04e211a32105/content
download
https://doi.org/10.26008/1912/bco-dmo.940678.1
download
onLine
dataset
<p>Microsatellites were amplified from DNA extracted from both hemocyte and tissue using Taq polymerase (Genesee Scientific) for a select number of basket cockles (Clinocardium nuttallii, urn:lsid:marinespecies.org:taxname:381980) colelcted from multipl intertidal locations in Washington State, USA. All possible neoplastic animals based on positive qPCR screen (n=26) and one randomly selected, non-neoplastic animal from each collection (n=12) were selected for microsatellite amplification and fragment analysis. Microsatellites were amplified using primers for 8 polymorphic loci: Cnu48, Cnu55, Cnu58, Cnu63, Cnu68, Cnu72, Cnu78, and Cnu81.&nbsp;<br />
<br />
Instrument Description:&nbsp;Allele sizes were identified by fragment analysis using fluorescent primers (6-FAM, PET, NED, and VIC) and a 3730xl Genetic Analyzer with the LIZ-500 size standard.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Data uploaded are raw data files, before processing.</p>
Specified by the Principal Investigator(s)
* All .fsa files submitted to BCO-DMO under folder "All Cnu microsatellites combined/" were bundled into "All_Cnu_microsatellites_combined.zip."
* Site information and collection metadata was extracted from a tab delimited table provided in metadata and imported into the BCO-DMO data system as a table. A location's lat,lon was revised based on the data submitter's input ("48 58,999", "-122 47,608" ->"48.98332", "-122.79347").
* ISO datetime with timezone added in UTC time zone (converted using the local date and time provided by submiter in PST/PDT).
* A file inventory was created including md5sum. The site_code was extracted as a dedicated column using the file prefix. The site_code was used to join the metadata table after verifying site_code was a unique key in the metadata table. File inventory and combined collection metadata attached to teh dataset as "940678_v1_cnu-microsatellites.csv"
* The Sample/Collection table alone was also attached as a supplemental file (row per site/collection).
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Rows with site code "SBg" were dropped at data submitter's requrest. (see Problems/Issues section)
Specified by BCO-DMO Data Managers
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
3730xl Genetic Analyzer with the LIZ-500 size standard
3730xl Genetic Analyzer with the LIZ-500 size standard
PI Supplied Instrument Name: 3730xl Genetic Analyzer with the LIZ-500 size standard 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.