http://lod.bco-dmo.org/id/dataset/728427
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
2018-02-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Data relating to RNA sequence accessions at NCBI from Ross Sea Dinoflagellates, Phaeocystis antarctica, Pyramimons tychotreta, and Micromonas polaris (CCMP 2099) (Kleptoplasty project)
2018-05-17
publication
2018-05-17
revision
BCO-DMO Linked Data URI
2018-05-17
creation
http://lod.bco-dmo.org/id/dataset/728427
Rebecca J. Gast
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: Gast, R. J. (2018) Data relating to RNA sequence accessions at NCBI from Ross Sea Dinoflagellates, Phaeocystis antarctica, Pyramimons tychotreta, and Micromonas polaris (CCMP 2099) (Kleptoplasty project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-05-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/728427 [access date]
Dataset Description: <p>This dataset contains data related to RNA sequence genetic accessions at the National Center for Biotechnology Information (NCBI) including information about the host organism, collection location, and collection date.&nbsp;&nbsp;</p>
<p>The&nbsp;accessions are the unprocessed Illumina MiSeq reads for the Ross Sea Dinoflagellate RNA-Seq experiments, <em>Phaeocystis antarctica</em> RNA-Seq experiments, and <em>Pyramimons tychotreta</em> &amp; <em>Micromonas polaris</em>&nbsp;(CCMP 2099) mixotrophy experiments.</p>
<p><em>Pyramimonas&nbsp;tychotreta</em>&nbsp;&amp;&nbsp;<em>Micromonas&nbsp;polaris</em>&nbsp;(CCMP 2099) mixotrophy RNA sequences are available through the NCBI Sequence Read Archive (SRA) under the SRA accession number <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP090401" target="_blank">SRP090401</a> (BioProject <a href="https://www.ncbi.nlm.nih.gov//bioproject/PRJNA342459" target="_blank">PRJNA342459</a>)</p>
<p>Ross Sea Dinoflagellate RNA sequences are available through the NCBI Sequence Read Archive&nbsp;(SRA)&nbsp;under the accession number <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP132912" target="_blank">SRP132912</a> (BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/428208" target="_blank">PRJNA428208</a>).</p>
<p>Phaeocystis antarctica RNA sequences&nbsp;are available through the NCBI Sequence Read Archive&nbsp;(SRA)&nbsp;under the accession number <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP133243" target="_blank">SRP133243</a> (BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/434497" target="_blank">PRJNA434497</a>).</p> Methods and Sampling: <p><strong><em>Pyramimonas tychotreta</em> and <em>Micromonas polaris</em> (CCMP 2099) mixotrophy RNA-Seq</strong></p>
<p>Replicate cultures (n=4 for each isolate and treatment) were incubated under high- and reduced-nutrient conditions for a week.&nbsp; High-nutrient treatments were full strength f/2+Si (i.e., the maintenance media), while low-nutrient treatments were a 10-fold dilution of f/2 + Si culture media with filter-sterilized seawater. The low-nutrient conditions were previously found to elicit increases in ingestion by these two species.</p>
<p><strong>Ross Sea Dinoflagellate and <em>Phaeocystis </em></strong><em><strong>antarctica</strong></em><strong> RNA-Seq</strong></p>
<p>The Ross Sea Dinoflagellate (RSD) was enriched away from the prey and grown in f/2 + Si at 0C under 14/10hr light dark cycle at 26.2 µmol/m2/sec. For the temperature experiment, flasks with approximately 450,000 cells each incubated at 0C (4 replicates) or 5C (4 replicates) for 5 days.&nbsp; For the different light conditions, flasks of approximately 450,000 cells each were incubated under constant illumination of 371 µmol/m2/sec (surface; 4 replicates), 48 µmol/m2/sec (DCM; 4 replicates) or darkness (4 replicates) at 0C for 5 days.</p>
<p><em>Phaeocystis antarctica</em> was grown under the same experimental conditions with 4 replicates per treatment.&nbsp; Approximately 3.3 x 10^6 cells per replicate were used in the 0C incubation, 2.6 x 10^6 cells per replicate in the 5C incubation, and 1.4 x 10^7 cells per replicate in the different light exposure treatments.</p>
<p><strong>Sampling and analytical procedures: </strong></p>
<p><em>Pyramimonas</em> and <em>Micromonas</em> were collected on 25mm 0.2 µm polycarbonate filters, frozen at -80°C, then extracted using the Qiagen Mini RNA kit, with confirmation of nucleic acid abundance and quality assessed by Bioanalyzer. Replicate samples were sent to the Sulzberger Genome Center at Columbia University for poly-A selection, library construction and sequencing by Illumina Mi-Seq (150bp paired-end reads, 30 million reads per sample).</p>
<p>RSD and <em>Phaeocystis</em> cultures were fixed with RNALater and harvested by filtration onto 0.8 micron pore size 25 mm polycarbonate filters. Cells were lysed using the Qiagen RNeasy Mini Kit.&nbsp; DNA was removed by DNase treatment on the purification column.&nbsp; mRNA was isolated using ribosomal depletion (Ribo-Zero™ rRNA Removal Kit for Plant Leaf).&nbsp; RNA quality was checked by Bioanalyzer and sent to Sulzberger Columbia Genome Center for library preparation and RNA-Seq (150bp paired-end reads, 30 million reads per sample).</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1341362 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1341362
completed
Rebecca J. Gast
Woods Hole Oceanographic Institution
508-289-3209
266 Woods Hole Rd. MS #32
Woods Hole
MA
02543
USA
rgast@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject_descrip
SRA_Study
BioProject
BioProject_link
Experiment
Library_Name
Sample_Name
Assay_Type
LibrarySelection
replicate
BioSample
Organism
collection_date
geo_loc_name
isolate
sample_type
collected_by
culture_collection
depth
identified_by
lat
lon
temp
Illumina Mi-Seq
theme
None, User defined
brief description
accession number
external_link
experiment id
sample description
replicate
date
site description
person name
depth
latitude
longitude
water temperature at measurement depth
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.
You are what you eat: The Role of Kleptoplasty in an Antarctic Dinoflagellate
https://osprey.bco-dmo.org/project/568443
You are what you eat: The Role of Kleptoplasty in an Antarctic Dinoflagellate
<p><em>Description from NSF award abstract:</em><br />
Kleptoplasty, the temporary acquisition and use of functional chloroplasts derived from algal prey, is viewed as an important model for the early evolution of the permanent, endosymbiotically-derived chloroplasts found in all permanently photosynthetic eukaryotes. This project will study the evolutionary history and expression of plastid-targeted genes in an abundant Antarctic dinoflagellate that steals chloroplasts from an ecologically important alga, the haptophyte Phaeocystis. Algae play an important role in the fixation and export of CO2 in the Southern Ocean, and this project will explore the genetic basis for the function of these chimeric cells with regard to their functional adaptation to extreme environments and will study the evolutionary history and expression of plastid-targeted genes in both the host and recipient. The project seeks to determine whether the kleptoplastidic dinoflagellate utilizes ancestral plastid proteins to regulate its stolen plastid, and how their transcription is related to environmental factors that are relevant to the Southern Ocean environment (temperature and light). To accomplish these goals, the project will utilize high throughput transcriptome analysis and RNA-sequencing experiments with the dinoflagellate and Phaeocystis.</p>
<p>This work will help biologists understand the environmental success of this alternative nutritional strategy, and to assess the potential impact of anthropogenic climate change on the organism. The project will also contribute to the maintenance of a culture collection of heterotrophic, phototrophic and mixotrophic Antarctic protists that are available to the scientific community, and it will support the mentoring of a graduate student and a postdoctoral fellow. The work is being accomplished as an international collaboration between US and Canadian scientists, and in addition to publishing results in peer-reviewed journals, the investigators will incorporate aspects of this work into public outreach activities. These include field data analysis opportunities for middle school students and science-based art projects with local schools and museums.</p>
Kleptoplasty
largerWorkCitation
project
eng; USA
oceans
162
-74.75
-78
76.2833
1997-12-01
1998-04-07
Ross Sea, Antarctica
0
BCO-DMO catalogue of parameters from Data relating to RNA sequence accessions at NCBI from Ross Sea Dinoflagellates, Phaeocystis antarctica, Pyramimons tychotreta, and Micromonas polaris (CCMP 2099) (Kleptoplasty 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/735928.rdf
Name: BioProject_descrip
Units: unitless
Description: <p>Brief description of BioProject</p>
http://lod.bco-dmo.org/id/dataset-parameter/735929.rdf
Name: SRA_Study
Units: unitless
Description: <p>SRA Study accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/735930.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject number. A BioProject is a collection of biological data related to a single initiative originating from a single organization or from a consortium</p>
http://lod.bco-dmo.org/id/dataset-parameter/735931.rdf
Name: BioProject_link
Units: unitless
Description: <p>Link to the NCBI BioProject page</p>
http://lod.bco-dmo.org/id/dataset-parameter/735932.rdf
Name: Experiment
Units: unitless
Description: <p>Experiment identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/735933.rdf
Name: Library_Name
Units: unitless
Description: <p>Library name</p>
http://lod.bco-dmo.org/id/dataset-parameter/735934.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/735935.rdf
Name: Assay_Type
Units: unitless
Description: <p>Assay type</p>
http://lod.bco-dmo.org/id/dataset-parameter/735936.rdf
Name: LibrarySelection
Units: unitless
Description: <p>Library Selection</p>
http://lod.bco-dmo.org/id/dataset-parameter/735937.rdf
Name: replicate
Units: unitless
Description: <p>Replicate name</p>
http://lod.bco-dmo.org/id/dataset-parameter/735938.rdf
Name: BioSample
Units: unitless
Description: <p>Biosample accession number at NCBI (stores descriptive information about the physical biological materials)</p>
http://lod.bco-dmo.org/id/dataset-parameter/735939.rdf
Name: Organism
Units: unitless
Description: <p>Organism sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/735940.rdf
Name: collection_date
Units: unitless
Description: <p>Date sample was collected (various formats)</p>
http://lod.bco-dmo.org/id/dataset-parameter/735941.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographical origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/735942.rdf
Name: isolate
Units: unitless
Description: <p>Identification or description of the specific individual from which this sample was obtained</p>
http://lod.bco-dmo.org/id/dataset-parameter/735943.rdf
Name: sample_type
Units: unitless
Description: <p>Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/735944.rdf
Name: collected_by
Units: unitless
Description: <p>Name of persons or institute who collected the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/735945.rdf
Name: culture_collection
Units: unitless
Description: <p>Institution code and identifier for the culture from which the nucleic acid sequenced was obtained (see <a href="http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier">http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/735946.rdf
Name: depth
Units: unitless
Description: <p>Depth (vertical distance below surface)</p>
http://lod.bco-dmo.org/id/dataset-parameter/735947.rdf
Name: identified_by
Units: unitless
Description: <p>Name of the taxonomist who identified the specimen</p>
http://lod.bco-dmo.org/id/dataset-parameter/735948.rdf
Name: lat
Units: decimal degrees
Description: <p>Collection latitude of sampled organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/735949.rdf
Name: lon
Units: decimal degrees
Description: <p>Collection longitude of sampled organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/735950.rdf
Name: temp
Units: degrees Celsius
Description: <p>Water temperature at organism collection location</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
16993
https://datadocs.bco-dmo.org/file/8XXgn3pUpplDo/SRA_toplevel.csv
SRA_toplevel.csv
Primary data file for dataset ID 728427
download
https://osprey.bco-dmo.org/dataset/728427/data/download
download
onLine
dataset
<p><strong><em>Pyramimonas tychotreta</em> and <em>Micromonas polaris</em> (CCMP 2099) mixotrophy RNA-Seq</strong></p>
<p>Replicate cultures (n=4 for each isolate and treatment) were incubated under high- and reduced-nutrient conditions for a week.&nbsp; High-nutrient treatments were full strength f/2+Si (i.e., the maintenance media), while low-nutrient treatments were a 10-fold dilution of f/2 + Si culture media with filter-sterilized seawater. The low-nutrient conditions were previously found to elicit increases in ingestion by these two species.</p>
<p><strong>Ross Sea Dinoflagellate and <em>Phaeocystis </em></strong><em><strong>antarctica</strong></em><strong> RNA-Seq</strong></p>
<p>The Ross Sea Dinoflagellate (RSD) was enriched away from the prey and grown in f/2 + Si at 0C under 14/10hr light dark cycle at 26.2 µmol/m2/sec. For the temperature experiment, flasks with approximately 450,000 cells each incubated at 0C (4 replicates) or 5C (4 replicates) for 5 days.&nbsp; For the different light conditions, flasks of approximately 450,000 cells each were incubated under constant illumination of 371 µmol/m2/sec (surface; 4 replicates), 48 µmol/m2/sec (DCM; 4 replicates) or darkness (4 replicates) at 0C for 5 days.</p>
<p><em>Phaeocystis antarctica</em> was grown under the same experimental conditions with 4 replicates per treatment.&nbsp; Approximately 3.3 x 10^6 cells per replicate were used in the 0C incubation, 2.6 x 10^6 cells per replicate in the 5C incubation, and 1.4 x 10^7 cells per replicate in the different light exposure treatments.</p>
<p><strong>Sampling and analytical procedures: </strong></p>
<p><em>Pyramimonas</em> and <em>Micromonas</em> were collected on 25mm 0.2 µm polycarbonate filters, frozen at -80°C, then extracted using the Qiagen Mini RNA kit, with confirmation of nucleic acid abundance and quality assessed by Bioanalyzer. Replicate samples were sent to the Sulzberger Genome Center at Columbia University for poly-A selection, library construction and sequencing by Illumina Mi-Seq (150bp paired-end reads, 30 million reads per sample).</p>
<p>RSD and <em>Phaeocystis</em> cultures were fixed with RNALater and harvested by filtration onto 0.8 micron pore size 25 mm polycarbonate filters. Cells were lysed using the Qiagen RNeasy Mini Kit.&nbsp; DNA was removed by DNase treatment on the purification column.&nbsp; mRNA was isolated using ribosomal depletion (Ribo-Zero™ rRNA Removal Kit for Plant Leaf).&nbsp; RNA quality was checked by Bioanalyzer and sent to Sulzberger Columbia Genome Center for library preparation and RNA-Seq (150bp paired-end reads, 30 million reads per sample).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<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' for "no data" so they are recognized in our system<br />
* metadata for runs obtained with sra run selector results at NCBI to download files that have the biosample, bioproject, sra project and sample info in them.<br />
* split lat_lon into lat,lon in decimal degrees<br />
* commas replaced with ;<br />
* added link to each BioProject at NCBI</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 Mi-Seq
Illumina Mi-Seq
PI Supplied Instrument Name: Illumina Mi-Seq 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.