http://lod.bco-dmo.org/id/dataset/670912
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
2016-12-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for genetic sequences of virus-enriched field samples and P. carterae viruses from laboratory cultures at Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016
2016-12-21
publication
2016-12-21
revision
BCO-DMO Linked Data URI
2016-12-21
creation
http://lod.bco-dmo.org/id/dataset/670912
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
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: Martínez Martínez, J. (2016) Accession numbers for genetic sequences of virus-enriched field samples and P. carterae viruses from laboratory cultures at Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-12-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/670912 [access date]
Accession numbers for genetic sequences from virus-enriched field samples and P. carterae CCMP 645 culture co-infections Dataset Description: <p>This dataset contains assembled metagenomic contig information from viruses co-infecting a <em>P. carterae </em>CCMP 645 laboratory cultures and virus-enriched metagenomics contigs from &lt; 0.45 um-filtered seawater samples collected at the Bigelow Laboratory’s dock, at the Damariscotta River Estuary,&nbsp;Maine. Included in this dataset are accession identifiers for the National Center for Biotechnology Information (NCBI) where the sequence data is stored.</p>
<p>When data is unrestricted an update to the data will be made to provide direct links to accession information at NCBI.</p>
<p><strong>Related datasets:</strong><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670431" target="_blank">Pleurochrysis carterae growth</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670442">Pleurochrysis carterae virus production</a><br />
*&nbsp;&nbsp;<a href="https://www.bco-dmo.org/dataset/670450" target="_blank">Virus dPCR assay primers</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670714" target="_blank">TEM Pleurochrysis carterae thin section images</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670706" target="_blank">TEM Pleurochrysis carterae virion images</a></p> Methods and Sampling: <p><strong>Laboratory cultured&nbsp;<em>P. carterae&nbsp;</em>CCMP 645 viruses</strong></p>
<p>A 2 L culture of <em>P. carterae </em>CCMP 645 in exponential growth phase, grown in F/2 medium was filtered through a 0.2 um PES membrane under sterile conditions. The filtrate was then initially concentrated down to approximately 25 ml by tangential flow filtration using a Vivaflow 50 cartridge (Sartorius) and further concentrated down to approximately 1 ml using a 30 kDa MWCO AmiconUltra-15 column (Millipore).</p>
<p>DNA&nbsp;from the viral concentrate was extracted using the QiaAMP MinElute Virus spin kit. DNA was tested with universal 16S and 18S primer sets and determined to be free of host, or prokaryotic contamination prior to sequencing.</p>
<p>Two independent sequencing libraries were prepared and sequenced by Illumina MiSeq platforms through Bigelow Laboratory for Ocean Sciences’ Single Cell Genomic Center (150 bp paired-end reads) and through the Sequencing Facility at the University of Wisconsin-Madison (300 bp paired-end reads). In addition, PCR products generated to join contig ends were pooled and sequenced in 3 batches (MiSeq), also generating 300 bp paired ends through the University of Wisconsin-Madison.&nbsp;</p>
<p><strong>Virus-enriched Bigelow Dock sample metagenome:</strong></p>
<p>Six large, land-based, 2460 dm-3 volume mesocosm tanks were filled on September 24, 2015, from a seawater supply at Bigelow Laboratory’s deep-water dock site at the&nbsp;Damariscotta River Estuary,&nbsp;Maine. The samples were&nbsp;screened through 3 mm mesh, with care taken to ensure that each tank was filled simultaneously and contained the same starting phytoplankton composition. The mesocosms were aimed for testing the effects of climate change by simulating predicted increasing temperature and pCO2 environments in the Gulf of Maine over the next several centuries. However, for our study 1 L samples were collected from each of the mesocosms on Day 0 prior to any further experimental manipulation. All six liters were combined and virus-enriched by filtering through a 0.45 um PES filter to remove most cellular organisms, and concentrated down to 45 ml by tangential flow filtration. Total DNA was extracted from the sample using the MasterPure(TM) Complete DNA and RNA Purification kit (Epicentre) following manufacturer’s recommendations. Total DNA was eluted in 20 ul of nuclease-free water. A DNA library was prepared and sequenced by Illumina MiSeq.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1346272 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1346272
onGoing
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
410-221-1819
2020 Horns Point Road AREL 239
Cambridge
MD
21613
USA
jmartinez@umces.edu
pointOfContact
asNeeded
Unknown
accession_id
organism_name
location_collected
date_collected
sequencing_method
analysis_method
sequence_description
Illumina MiSeq
Bio Rad icycler
theme
None, User defined
accession number
sample description
site
date
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Bigelow_Martinez_2015-2016
service
Deployment Activity
Bigelow Laboratory for Ocean Sciences, Maine
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.
Persistent Virus Infections in Marine Phytoplankton
https://osprey.bco-dmo.org/project/560443
Persistent Virus Infections in Marine Phytoplankton
<p><em>Description from NSF award abstract:</em><br />
Viruses are prevalent in every part of the environment of our living planet, and yet our understanding of type, distribution, and function is the least well-known aspect of biodiversity. In recent years we have developed an increased appreciation for the role viruses play in driving host evolution in the environment, but fundamental knowledge about the mechanisms involved remain lacking. Additionally, viruses may influence diversity indirectly through "kill the winner" scenarios, as well as through cell lysis and subsequent release of dissolved nutrients, which facilitate restructuring of microbial communities. The majority of research on marine viruses to date has focused on combinations of acutely susceptible host strains with highly virulent virus isolates. However, it is likely that marine viruses also employ a persistent infection life strategy, arguably preferring it to the more widely recognized lytic cycle. The objective of this project is to demonstrate that persistent virus infections occur in marine phytoplankton, and that these are a crucial component of ocean ecosystem function and a key evolutionary driver in primary producers. Using a range of persistent virus:host systems, this project will investigate:<br />
1) how pervasive persistent virus infections are in marine systems; and<br />
2) the role of non-coding RNAs in maintaining host:virus symbiosis.</p>
<p>This is a high risk-high pay research as it involves a radically different approach to the analysis of viruses in marine systems. The investigators plan to apply a suite of molecular (transcriptomics, genomics and development of novel diagnostic markers) techniques to include the analysis of microRNAs to determine the functional importance of persistent viruses in the ocean. The results of this project will be potentially transformative for our understanding of virus-driven phytoplankton evolution and its potential impact on biodiversity in marine phytoplankton, a vital component of the global carbon cycle.</p>
<p>Note: William Wilson (Bigelow Laboratory) was the Former Principal Investigator on this project award.</p>
Marine Chronic Viruses
largerWorkCitation
project
eng; USA
oceans
Bigelow Laboratory for Ocean Sciences, Maine
2016-12-21
0
BCO-DMO catalogue of parameters from Accession numbers for genetic sequences of virus-enriched field samples and P. carterae viruses from laboratory cultures at Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016
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/670920.rdf
Name: accession_id
Units: unitless
Description: <p>NCBI identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/670921.rdf
Name: organism_name
Units: unitless
Description: <p>description of virus or metagenome sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/670922.rdf
Name: location_collected
Units: unitless
Description: <p>location of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/670923.rdf
Name: date_collected
Units: unitless
Description: <p>date of sample collection in format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/670924.rdf
Name: sequencing_method
Units: unitless
Description: <p>Method of sequence generation (e.g. illumina MiSeq)</p>
http://lod.bco-dmo.org/id/dataset-parameter/670925.rdf
Name: analysis_method
Units: unitless
Description: <p>description of analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/670926.rdf
Name: sequence_description
Units: unitless
Description: <p>description of sequence indicating type (ssDNA/dsDNA) and completeness of sequence (partial/complete)</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
3247
https://datadocs.bco-dmo.org/file/M77XP8Gu69QNGq/accessions.csv
accessions.csv
Primary data file for dataset ID 670912
download
https://osprey.bco-dmo.org/dataset/670912/data/download
download
onLine
dataset
<p><strong>Laboratory cultured&nbsp;<em>P. carterae&nbsp;</em>CCMP 645 viruses</strong></p>
<p>A 2 L culture of <em>P. carterae </em>CCMP 645 in exponential growth phase, grown in F/2 medium was filtered through a 0.2 um PES membrane under sterile conditions. The filtrate was then initially concentrated down to approximately 25 ml by tangential flow filtration using a Vivaflow 50 cartridge (Sartorius) and further concentrated down to approximately 1 ml using a 30 kDa MWCO AmiconUltra-15 column (Millipore).</p>
<p>DNA&nbsp;from the viral concentrate was extracted using the QiaAMP MinElute Virus spin kit. DNA was tested with universal 16S and 18S primer sets and determined to be free of host, or prokaryotic contamination prior to sequencing.</p>
<p>Two independent sequencing libraries were prepared and sequenced by Illumina MiSeq platforms through Bigelow Laboratory for Ocean Sciences’ Single Cell Genomic Center (150 bp paired-end reads) and through the Sequencing Facility at the University of Wisconsin-Madison (300 bp paired-end reads). In addition, PCR products generated to join contig ends were pooled and sequenced in 3 batches (MiSeq), also generating 300 bp paired ends through the University of Wisconsin-Madison.&nbsp;</p>
<p><strong>Virus-enriched Bigelow Dock sample metagenome:</strong></p>
<p>Six large, land-based, 2460 dm-3 volume mesocosm tanks were filled on September 24, 2015, from a seawater supply at Bigelow Laboratory’s deep-water dock site at the&nbsp;Damariscotta River Estuary,&nbsp;Maine. The samples were&nbsp;screened through 3 mm mesh, with care taken to ensure that each tank was filled simultaneously and contained the same starting phytoplankton composition. The mesocosms were aimed for testing the effects of climate change by simulating predicted increasing temperature and pCO2 environments in the Gulf of Maine over the next several centuries. However, for our study 1 L samples were collected from each of the mesocosms on Day 0 prior to any further experimental manipulation. All six liters were combined and virus-enriched by filtering through a 0.45 um PES filter to remove most cellular organisms, and concentrated down to 45 ml by tangential flow filtration. Total DNA was extracted from the sample using the MasterPure(TM) Complete DNA and RNA Purification kit (Epicentre) following manufacturer’s recommendations. Total DNA was eluted in 20 ul of nuclease-free water. A DNA library was prepared and sequenced by Illumina MiSeq.&nbsp;</p>
from Deployment: Bigelow_Martinez_2015-2016 <p>laboratory experiment</p>
Specified by the Principal Investigator(s)
<p>Each dataset was assembled independently then, co-assembled using Geneious (v. 8.1.6). De novo assembly pipeline was as follows:</p>
<p>1) Adapter removal and quality trimming using&nbsp;trimmomatic&nbsp;(1.0.32)<br />
2) Custom python script to merge paired reads into one file (fastx.py)<br />
3) Normalization using&nbsp;kmernorm&nbsp;(v. 1.0.5)<br />
4) Assembly with SPAdes (3.9.0) using the careful parameter and&nbsp;phred&nbsp;offset 33.<br />
5) Contigs were imported into Geneious and assembled using the Geneious assembler to help to stitch together contigs from separate sequencing efforts. Raw reads were aligned to the final contigs in&nbsp;geneious&nbsp;using the&nbsp;bwa&nbsp;aligner to validate the accuracy of the assembly.</p>
<p><strong>Laboratory cultured&nbsp;<em>P. carterae&nbsp;</em>CCMP 645 viruses:</strong></p>
<p>Contigs were analyzed through the MetaVir web server.&nbsp;</p>
<p><strong>Virus-enriched Bigelow Dock sample metagenome:</strong></p>
<p>Contigs were annotated with GeneMarkS, then checked manually for any missed potential open reading frames using Artemis. ORFs were blasted against nr, with an evalue threshold of E-5. All ORFs were also queried against hhpred for structural similarity and any hits were annotated accordingly.</p>
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><br />
* Combined field and culture accession datasets preserving relevant data about accession source<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values replaced with no data value 'nd'</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 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.
Bio Rad icycler
Bio Rad icycler
PI Supplied Instrument Name: Bio Rad icycler 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)
Deployment: Bigelow_Martinez_2015-2016
Bigelow_Martinez_2015-2016
lab Bigelow
laboratory
lab Bigelow
laboratory