http://lod.bco-dmo.org/id/dataset/885287
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
2022-12-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Test dataset created for testing and troubleshooting purposes
2025-11-30
publication
2025-11-30
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2025-11-13
publication
https://doi.org/10.83544/1912/bco-dmo.885287.1
Adam Shepherd
Florida State University - National High Magnetic Field Lab
principalInvestigator
Sawyer Newman
Woods Hole Oceanographic Institution
principalInvestigator
Karen Soenen
Woods Hole Oceanographic Institution
principalInvestigator
Shannon Rauch
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: Shepherd, A., Soenen, K., Newman, S., Rauch, S. (2025) Test dataset created for testing and troubleshooting purposes. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 18) Version Date 2025-11-26 [if applicable, indicate subset used]. doi:10.83544/1912/bco-dmo.885287.18 [access date]
Testing New Website Search again Dataset Description: <p>DNA extracts from the vicinity of Station ALOHA (22.75 N, 158.0 W) just north of Hawaii.</p>
<p><strong>CMORE RNA and DNA Archive </strong></p>
<p><strong>Goal:</strong> The goal of this effort is to provide a time series collection of planktonic microbial DNA and RNA depth profiles from the HOT station, for CMORE research. DNA and RNA samples will be available for researchers to conduct and coordinate taxonomic and functional gene studies, for example using PCR and RT-PCR methods. Where possible, metagenomic datasets will be generated by pyrosequencing for selected profiles, and posted for downloading the blast searching on the MIT-CMORE server (http://genesis2.mit.edu/).</p>
<p><strong>Activity:</strong> Collect microbial cell fraction (1.6um prefiltered, &gt;0.22um) from HOT hydrocasts, and extract nucleic acids, for RNA and DNA for downstream analyses by CMORE investigators. Collection depths are 25m, 45m, 75m, 125m, 200m, 500m, 770m and 1000m. Extracted DNA samples will be available for distribution.</p> Methods and Sampling: <p><strong>Sampling and analytical procedures: </strong></p>
<p>The genomes of two different individuals were sequenced with different approaches:</p>
<p>1. An individual sampled at Jekyll Island, Georgia:</p>
<p>We built a reference genome for the Atlantic silverside through three steps. First, we created a draft assembly using 10x Genomics linked-reads technology (10x Genomics, Pleasanton, CA). Second, we used proximity-ligation data— ChicagoVR (Putnam et al. 2016) and Dovetail</p>
<p>Hi-C (Lieberman-Aiden et al. 2009)—from Dovetail Genomics (Santa Cruz, CA) to increase contiguity, break up mis-joins, and orient and join scaffolds into chromosomes. Finally, we used short-insert reads to close gaps in the scaffolded and error-corrected assembly. The data were generated from muscle tissue dissected from two lab-reared F1 offspring of Atlantic silversides collected from the wild on Jekyll Island, GA, USA (N31.02 ,W81.43 ; the southern end of the species distribution range) in May 2017. For 10x Genomics library preparation, we extracted DNA from fresh tissue from one individual using the MagAttract HMW DNA Kit (Qiagen). Prior to library preparation, we selected fragments longer than 30 kb using a BluePippin device (Sage Science). A 10x Genomics library was prepared following standard procedure and sequenced using two lanes of paired-end 150 bp reads on a HiSeq2500 (rapid run mode) at the Biotechnology Resource Center Genomics Facility at Cornell University. To assemble the linked reads, we ran the program Supernova 2.1.1 (Weisenfeld et al. 2017) from 10x Genomics with varying numbers of reads and compared assembly statistics to identify the number of reads that resulted in the most contiguous assembly. Tissue from the second individual was flash frozen in liquid nitrogen and shipped to Dovetail Genomics, where Chicago and Hi-C libraries were prepared for further scaffolding. These long-range libraries were sequenced on one lane of Illumina HiSeqX using paired-end 150 bp reads. Two rounds of scaffolding with HiRiseTM, a software pipeline developed specifically for genome scaffolding with Chicago and Hi-C data, were run to scaffold and error-correct the best 10x Genomics draft assembly using Dovetail long-range data. Finally, the barcode-trimmed 10x Genomics reads were used to close gaps between contigs as the final step of the HiRise pipeline.</p>
<p>2. An individual sampled in Mumford Cove, Connecticut</p>
<p>This assembly was a lower-quality draft assembly used to identify structural variants in comparison to the chromosome-level assembly from the individual sampled in Georgia</p>
<p>The individual sampled for this assembly was sampled from Mumford Cove, Connecticut (N 41.32 , W 72.02 ) in June 2016. Genomic DNA was extracted from muscle tissue using the DNeasy Blood and Tissue kit (Qiagen) and normalized to 40 ng/ul. We prepared a genomic DNA library using the TruSeq DNA PCR-free library kit (Illumina) following the manufacturer’s protocol for 550 bp insert libraries. The shotgun library was sequenced using paired-end 150 bp reads on an Illumina HiSeq4000. Mate- pair libraries with insert sizes of 3, 5.3, and 8.2 kb were pre- pared at the Huntsman Cancer Institute at the University of Utah using the Nextera Mate Pair Library Prep Kit (Illumina) and sequenced using paired-end 125 bp reads on an Illumina HiSeq2500. We used Trimmomatic 0.36 (Bolger et al. 2014) to remove adapter contamination and low-quality data from both the shotgun and the mate pair libraries and used these filtered reads to assemble a draft assembly and fill assembly gaps with Platanus v.1.2.4 (Kajitani et al. 2014) with the commands assemble, scaffold, and gap_close. Finally,we filtered scaffolds shorter than 1 kb.</p>
<p>Further details of the samples and methodology are available in the following publication:</p>
<p>Tigano, A., Jacobs, A., Wilder, A. P., Nand, A., Zhan, Ye, Dekker, J., and Therkildsen, N. O. 2021. Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation. <strong>Genome Biology and Evolution</strong> 13, evab163</p>
<p><strong>Super and subscript display test</strong><br />
&nbsp;</p>
<p>subscripts:</p>
<p>Our experiment assessed the CO<sub>2</sub>&nbsp;sensitivity of embryos and early life stages of BSB at a single static temperature (22°C) and three&nbsp;<em>p</em>CO<sub>2</sub>&nbsp;conditions (~400, ~2200, ~4200 µatm). On May 23<sup>rd</sup>, 2022, we strip-spawned wild, running-ripe BSB ((N<sub>female/male&nbsp;</sub>= 4/3) to produce viable embryos. Upon water-hardening a 5 ml sample of eggs was randomly allocated to a replicate 19-l rearing container held within one of nine recirculating systems within the Baumann labs automated larval rearing system (ALFiRiS).</p>
<p><br />
superscripts:<br />
<br />
At the late-exponential phase, cultures were transferred in triplicate to one of two SN media: (1) +P<em>i</em>&nbsp;(45 µmol L<sup>-1</sup>&nbsp;KH<sub>2</sub>PO<sub>4</sub>, following</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924618 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924618
onGoing
Adam Shepherd
Florida State University - National High Magnetic Field Lab
508-289-2772
ashepherd@whoi.edu
pointOfContact
Sawyer Newman
Woods Hole Oceanographic Institution
snewman@whoi.edu
pointOfContact
Karen Soenen
Woods Hole Oceanographic Institution
ksoenen@whoi.edu
pointOfContact
Shannon Rauch
Woods Hole Oceanographic Institution
508-289-2817
266 Woods Hole Rd. MS #36
Woods Hole
MA
02543
United States
srauch@whoi.edu
pointOfContact
asNeeded
Dataset Version: 19j
Unknown
HOT_cruises
service
Deployment Activity
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.
BCO-DMO: Accelerating Scientific Discovery through Adaptive Data Management
https://osprey.bco-dmo.org/project/824782
BCO-DMO: Accelerating Scientific Discovery through Adaptive Data Management
<p>NSF Award Abstract:</p>
<p>Scientific research is intrinsically reliant upon the creation, management, analysis, synthesis, and interpretation of data. Once generated, data are essential to demonstrating the veracity and reproducibility of scientific results, and existing data hold great potential to accelerate scientific discovery through reuse. The Biological and Chemical Oceanography and Data Management Office (BCO-DMO) was created in 2006 to assemble, curate, and publicly serve all data and related products resulting from grants funded by the NSF core programs for Biological and Chemical Oceanography, and Office of Polar Programs. BCO-DMO provides limnological and marine chemical, biological, and physical data inventories from several large and intermediate-sized programs, as well as single-investigator projects to support cross-disciplinary collaboration to address pressing environmental questions, problems, and challenges that are exacerbated with the increasing pace of climate change. BCO-DMO is committed to data management capacity building efforts, improving data literacy and increasing science engagement in data management topics through education, training, and outreach. The project collaborates with academic institutions and teachers, where the BCO-DMO database is leveraged for oceanographic curricula, and engages in targeted training of informatics students, cross-pollinating their knowledge with geoscience domain data management.</p>
<p>
BCO-DMO's goal is to facilitate the integration of its diverse datasets to enable researchers to achieve a deeper understanding of ocean ecological and biogeochemical systems. As a domain repository, BCO-DMO adds value and improves interoperability of data to support activities such as synthesis and modeling, and the reuse of oceanographic data for new research. Open access to the BCO-DMO database lowers barriers to allow economically challenged countries to gain access to research quality data for field decision support, policy-relevant issues, and educational purposes. The project takes an active role in the exchange of knowledge at national and international geoscience and informatics meetings and workshops, where standards development and adoption occur. BCO-DMO also participates in the development and use of open-source, standards-based technologies that enable interoperable data systems to exchange data and information that will foster next-generation research in all disciplines. While continuing to perform its core mission of data management, BCO-DMO will reconstitute its data infrastructure to mobilize a new adaptive data management strategy for addressing the evolutionary change coinciding with the big data revolution. Leveraging data semantics BCO-DMO will construct a knowledge graph for sustainably operating an adaptive data repository. This infrastructure will support dataset-level and repository-level metrics, an improved data submission experience and new data and metadata access capabilities. Through declarative workflows, the processing of contributed data will increase in efficiency, and result in actionable provenance records for complete transparency of data curation practices. Taking a holistic perspective on education, outreach and community engagement, formalized programs will be developed to promote data reuse and interest in oceanographic science.</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>
BCO-DMO
largerWorkCitation
project
eng; USA
oceans
-45
-30
60
65
2020-01-01
2024-04-03
0
BCO-DMO catalogue of parameters from Test dataset created for testing and troubleshooting purposes
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
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://doi.org/10.83544/1912/bco-dmo.885287.1
download
onLine
dataset
<p><strong>Sampling and analytical procedures: </strong></p>
<p>The genomes of two different individuals were sequenced with different approaches:</p>
<p>1. An individual sampled at Jekyll Island, Georgia:</p>
<p>We built a reference genome for the Atlantic silverside through three steps. First, we created a draft assembly using 10x Genomics linked-reads technology (10x Genomics, Pleasanton, CA). Second, we used proximity-ligation data— ChicagoVR (Putnam et al. 2016) and Dovetail</p>
<p>Hi-C (Lieberman-Aiden et al. 2009)—from Dovetail Genomics (Santa Cruz, CA) to increase contiguity, break up mis-joins, and orient and join scaffolds into chromosomes. Finally, we used short-insert reads to close gaps in the scaffolded and error-corrected assembly. The data were generated from muscle tissue dissected from two lab-reared F1 offspring of Atlantic silversides collected from the wild on Jekyll Island, GA, USA (N31.02 ,W81.43 ; the southern end of the species distribution range) in May 2017. For 10x Genomics library preparation, we extracted DNA from fresh tissue from one individual using the MagAttract HMW DNA Kit (Qiagen). Prior to library preparation, we selected fragments longer than 30 kb using a BluePippin device (Sage Science). A 10x Genomics library was prepared following standard procedure and sequenced using two lanes of paired-end 150 bp reads on a HiSeq2500 (rapid run mode) at the Biotechnology Resource Center Genomics Facility at Cornell University. To assemble the linked reads, we ran the program Supernova 2.1.1 (Weisenfeld et al. 2017) from 10x Genomics with varying numbers of reads and compared assembly statistics to identify the number of reads that resulted in the most contiguous assembly. Tissue from the second individual was flash frozen in liquid nitrogen and shipped to Dovetail Genomics, where Chicago and Hi-C libraries were prepared for further scaffolding. These long-range libraries were sequenced on one lane of Illumina HiSeqX using paired-end 150 bp reads. Two rounds of scaffolding with HiRiseTM, a software pipeline developed specifically for genome scaffolding with Chicago and Hi-C data, were run to scaffold and error-correct the best 10x Genomics draft assembly using Dovetail long-range data. Finally, the barcode-trimmed 10x Genomics reads were used to close gaps between contigs as the final step of the HiRise pipeline.</p>
<p>2. An individual sampled in Mumford Cove, Connecticut</p>
<p>This assembly was a lower-quality draft assembly used to identify structural variants in comparison to the chromosome-level assembly from the individual sampled in Georgia</p>
<p>The individual sampled for this assembly was sampled from Mumford Cove, Connecticut (N 41.32 , W 72.02 ) in June 2016. Genomic DNA was extracted from muscle tissue using the DNeasy Blood and Tissue kit (Qiagen) and normalized to 40 ng/ul. We prepared a genomic DNA library using the TruSeq DNA PCR-free library kit (Illumina) following the manufacturer’s protocol for 550 bp insert libraries. The shotgun library was sequenced using paired-end 150 bp reads on an Illumina HiSeq4000. Mate- pair libraries with insert sizes of 3, 5.3, and 8.2 kb were pre- pared at the Huntsman Cancer Institute at the University of Utah using the Nextera Mate Pair Library Prep Kit (Illumina) and sequenced using paired-end 125 bp reads on an Illumina HiSeq2500. We used Trimmomatic 0.36 (Bolger et al. 2014) to remove adapter contamination and low-quality data from both the shotgun and the mate pair libraries and used these filtered reads to assemble a draft assembly and fill assembly gaps with Platanus v.1.2.4 (Kajitani et al. 2014) with the commands assemble, scaffold, and gap_close. Finally,we filtered scaffolds shorter than 1 kb.</p>
<p>Further details of the samples and methodology are available in the following publication:</p>
<p>Tigano, A., Jacobs, A., Wilder, A. P., Nand, A., Zhan, Ye, Dekker, J., and Therkildsen, N. O. 2021. Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation. <strong>Genome Biology and Evolution</strong> 13, evab163</p>
<p><strong>Super and subscript display test</strong><br />
&nbsp;</p>
<p>subscripts:</p>
<p>Our experiment assessed the CO<sub>2</sub>&nbsp;sensitivity of embryos and early life stages of BSB at a single static temperature (22°C) and three&nbsp;<em>p</em>CO<sub>2</sub>&nbsp;conditions (~400, ~2200, ~4200 µatm). On May 23<sup>rd</sup>, 2022, we strip-spawned wild, running-ripe BSB ((N<sub>female/male&nbsp;</sub>= 4/3) to produce viable embryos. Upon water-hardening a 5 ml sample of eggs was randomly allocated to a replicate 19-l rearing container held within one of nine recirculating systems within the Baumann labs automated larval rearing system (ALFiRiS).</p>
<p><br />
superscripts:<br />
<br />
At the late-exponential phase, cultures were transferred in triplicate to one of two SN media: (1) +P<em>i</em>&nbsp;(45 µmol L<sup>-1</sup>&nbsp;KH<sub>2</sub>PO<sub>4</sub>, following</p>
Specified by the Principal Investigator(s)
<p>All files except those listed with “genome assembly” in the date type column are raw sequence data files that have not undergone any processing.</p>
<p>&nbsp;</p>
<p>The two genome assemblies were processed as described under “Sampling and analytical procedures” described above.</p>
Specified by the Principal Investigator(s)
BCO-DMO Processing
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
Cruise: HOT_cruises
HOT_cruises
Multiple Vessels
vessel
HOT_cruises
Angelicque E. White
University of Hawaiʻi at Mānoa
http://hahana.soest.hawaii.edu/hot/
Report describing HOT_cruises
Multiple Vessels
vessel