http://lod.bco-dmo.org/id/dataset/949666
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
2025-01-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metadata for longread sequencing of Carcinus maenas collected from Buzzards Bay, Massachusetts from May 2022 to Aug 2022
2025-01-29
publication
2025-01-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-11
publication
https://doi.org/10.26008/1912/bco-dmo.949666.1
Carolyn Tepolt
Woods Hole Oceanographic Institution
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: Tepolt, C. (2025) Metadata for longread sequencing of Carcinus maenas collected from Buzzards Bay, Massachusetts from May 2022 to Aug 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-01-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949666.1 [access date]
Metadata for longread sequencing of Carcinus maenas Dataset Description: Methods and Sampling: <p>Samples of&nbsp;<em>Carcinus maenas</em>&nbsp;(urn:lsid:marinespecies.org:taxname:107381)&nbsp;were collected between May 2022 and Aug 2022 from&nbsp;Massachusetts waters.&nbsp;</p>
<p>Extractions were performed with an NEB Monarch HMW DNA Extraction Kit for Cells &amp; Blood (May runs; low success) or a Circulomics Nanobind Tissue Big DNA kit (June and August runs; good success). Library prep was performed with a Oxford Nanopore Cas9 sequencing kit and custom Cas9 probes targeting putative inversion regions. May and June runs used the same first-round set of probes, while August runs used an updated second-round set of probes.&nbsp;Probe sequences are included in the supplemental file and can be cross-referenced using the probe_set value, though targeting is imperfect so much of the data simply reflect non-targeted genome sequencing. Libraries were sequenced on a single flowcell of an Oxford Nanopore MinION mk1c. For each round of sequencing (May, June, and August), the same library was run twice for 24 hours each time, with a flowcell flush at 24 hours. The run_day value captures this, listing this pre- and post-flush runs as run_days 1 and 2, respectively, for each single sample.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850996 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850996
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850945 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850945
completed
Carolyn Tepolt
Woods Hole Oceanographic Institution
5082893542
266 Woods Hole Road
Woods Hole
MA
025431535
US
ctepolt@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
Collection_date
SRA_accession
biosample_accession
embayment
state
sex
life_stage
run_ID
sequencing_date
run_day
probe_set
Oxford Nanopore MinION mk1c.
theme
None, User defined
sample identification
date
NCBI SRA run accession (SRR)
NCBI BioSample accession
site
region
sex
stage
experiment id
time_elapsed
featureType
BCO-DMO Standard Parameters
Nanopore 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.
Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator
https://osprey.bco-dmo.org/project/811534
Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator
<p><em><strong>NSF Award Abstract: </strong></em><br />
Marine invasive species pose a serious and ongoing risk to ocean ecosystems and the economies that rely on them. Understanding how such species adapt rapidly to new environments is key to preventing and managing invasions. Traditionally, the focus has been on inherent traits and flexibility of an invasive species, ignoring the potential for evolutionary change after introduction. However, recent research has shown that some marine species may evolve specific genomic features which allow highly efficient selection over as little as a single generation. This project tests the importance of genomic traits in allowing marine invasive species to survive and thrive on new shores. Its focus is on the high-impact invasive European green crab, which has spread over 1,500 km of the West Coast of North America since 1989 and has very recently begun expanding into the Salish Sea. This project tracks the earliest stages of green crab invasion into a new environment where the species is predicted to have substantial ecological and economic impacts. Genetic differences are followed over time and space across the entire West Coast, with a focus on crabs found in the Salish Sea where the species is currently expanding. Genetic data is complemented by oceanographic modeling to predict the spread of green crabs into the Salish Sea and across the West Coast. Finally, targeted sequencing and prior sampling are used to probe the genomic traits underlying these changes and determine if the same traits have played a role in the species' invasive success on other shores. Sampling for this project is conducted by Washington Sea Grant's Crab Team, an expansive outreach and monitoring program powered largely by hundreds of volunteers who monitor green crabs across 3,000 miles of coastline in the Salish Sea. The results of this project are shared with these volunteers and other stakeholders and is used to inform trans-boundary green crab management and spread prediction on the West Coast.</p>
<p>Recent work has hypothesized that genomic architecture, which has been increasingly discovered to play a role in local adaptation, may also be key to a species' ability to adapt quickly when gene flow is high. This project integrates multiple approaches to track the speed and dynamics of adaptation-with-gene flow across a thermal gradient in an explicit oceanographic context using the invasive European green crab (Carcinus maenas). Prior work in this system identified a suite of genes that appear to constitute balanced polymorphisms whose allele frequencies correlate strongly with site temperature against a homogeneous neutral genetic background. This project has three main goals: 1) To examine fine-scale selection to temperature over a comprehensive spatial and temporal data set comprising most of the species' history on the West Coast, 2) To track the expanding range front in the Salish Sea, comparing the genetic trajectory of individuals at the range edge with oceanographic modeling of dispersal, and 3) To characterize the genomic regions surrounding putative balanced polymorphisms and examine the ubiquity of their association with temperature across globally replicated populations. This coupled evolutionary oceanography approach represents an unprecedented test of the speed and nature of rapid adaptation in a highly dynamic natural marine environment.</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>
West Coast Carcinus
largerWorkCitation
project
eng; USA
biota
oceans
-71.201019
-70.589905
41.30566
41.775408
2022-05-18
2022-08-08
North American west coast: 36 N to 51 N. Emphasis on the Salish Sea
0
BCO-DMO catalogue of parameters from Metadata for longread sequencing of Carcinus maenas collected from Buzzards Bay, Massachusetts from May 2022 to Aug 2022
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/949881.rdf
Name: sample_name
Units: unitless
Description: <p>Individual sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/949882.rdf
Name: Collection_date
Units: unitless
Description: <p>Date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/949883.rdf
Name: SRA_accession
Units: unitless
Description: <p>SRA accession number for individual sequence files</p>
http://lod.bco-dmo.org/id/dataset-parameter/949884.rdf
Name: biosample_accession
Units: unitless
Description: <p>Individual NCBI BioSample code</p>
http://lod.bco-dmo.org/id/dataset-parameter/949885.rdf
Name: embayment
Units: unitless
Description: <p>General coastal water body from which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/949886.rdf
Name: state
Units: unitless
Description: <p>US state or Canadian province where samples was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/949887.rdf
Name: sex
Units: unitless
Description: <p>Sex (M=Male, F=Female, or U=Unknown)</p>
http://lod.bco-dmo.org/id/dataset-parameter/949888.rdf
Name: life_stage
Units: unitless
Description: <p>Stage of life of sampe (Adult)</p>
http://lod.bco-dmo.org/id/dataset-parameter/949889.rdf
Name: run_ID
Units: unitless
Description: <p>Unique identifier for MinION run</p>
http://lod.bco-dmo.org/id/dataset-parameter/949890.rdf
Name: sequencing_date
Units: unitless
Description: <p>Date that first sequencing run was started</p>
http://lod.bco-dmo.org/id/dataset-parameter/949891.rdf
Name: run_day
Units: days
Description: <p>For a single sample, whether the data were collected on day 1 or 2 of sequencing, where a flow-cell flush was performed in between</p>
http://lod.bco-dmo.org/id/dataset-parameter/949892.rdf
Name: probe_set
Units: unitless
Description: <p>Set of Cas9 probes used to target sequencing (see additional file in this dataset)</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
796
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/811ded3a-3cb1-4ed5-8ac4-77a9ec6ddfdc/content
download
https://doi.org/10.26008/1912/bco-dmo.949666.1
download
onLine
dataset
<p>Samples of&nbsp;<em>Carcinus maenas</em>&nbsp;(urn:lsid:marinespecies.org:taxname:107381)&nbsp;were collected between May 2022 and Aug 2022 from&nbsp;Massachusetts waters.&nbsp;</p>
<p>Extractions were performed with an NEB Monarch HMW DNA Extraction Kit for Cells &amp; Blood (May runs; low success) or a Circulomics Nanobind Tissue Big DNA kit (June and August runs; good success). Library prep was performed with a Oxford Nanopore Cas9 sequencing kit and custom Cas9 probes targeting putative inversion regions. May and June runs used the same first-round set of probes, while August runs used an updated second-round set of probes.&nbsp;Probe sequences are included in the supplemental file and can be cross-referenced using the probe_set value, though targeting is imperfect so much of the data simply reflect non-targeted genome sequencing. Libraries were sequenced on a single flowcell of an Oxford Nanopore MinION mk1c. For each round of sequencing (May, June, and August), the same library was run twice for 24 hours each time, with a flowcell flush at 24 hours. The run_day value captures this, listing this pre- and post-flush runs as run_days 1 and 2, respectively, for each single sample.</p>
Specified by the Principal Investigator(s)
<p>Minimal initial processing&nbsp;with standard Oxford Nanopore MinKNOW software (v22.03.06) was used to convert native fast5 files into fastq format for downstream processing. Only the fastq files in the "pass" bin were shared to the SRA. The MinKNOW software&nbsp;includes the following subpackage versions: MinKNOW core v5.0.0, Guppy v6.0.7, Bream v7.0.9, and Script Configuration v5.0.8.</p>
Specified by the Principal Investigator(s)
- Imported "BCODMO_MinION_metadata_NSF-1850996.csv" into BCO-DMO system
- Converted "Collection_date" and "sequencing_date" to ISO 8601 format
- Exported resource as "949666_v1_longread_seq_metadata.csv"
Accepted species identifier confirmed on 2025-01-29.
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
Oxford Nanopore MinION mk1c.
Oxford Nanopore MinION mk1c.
PI Supplied Instrument Name: Oxford Nanopore MinION mk1c. PI Supplied Instrument Description:Sequencing was done with an Oxford Nanopore MinION mk1c. Instrument Name: Nanopore Sequencer Instrument Short Name: Instrument Description: A proprietary high-throughput DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence DNA molecules as they pass through nanopores, driven by electrophoresis.