http://lod.bco-dmo.org/id/dataset/636831
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
2016-01-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
ENA accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light (GeTFeHvCOdia project)
2016-01-28
publication
2016-01-28
revision
BCO-DMO Linked Data URI
2016-01-28
creation
http://lod.bco-dmo.org/id/dataset/636831
Bethany D. Jenkins
University of Rhode Island
principalInvestigator
Phoebe Dreux Chappell
Old Dominion University
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: Jenkins, B. D., Chappell, P. D. (2016) ENA accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light (GeTFeHvCOdia project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2016-01-28) Version Date 2016-01-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636831 [access date]
ENA accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light Dataset Description: <p><strong>Marine MicroEukaryote Transcriptome Sequencing Project (MMETSP) Sample Links:</strong><br />
iMicrobe accession: <a href="http://data.imicrobe.us/project/view/104" target="_blank">http://data.imicrobe.us/project/view/104</a><br />
GenBank SRA accession:&nbsp;<a href="http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA231566" target="_blank">http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA231566</a></p>
<p><strong>Related Datasets:</strong><br />
<a href="http://data-mgr.bco-dmo.org/dataset/636567" target="_blank">Thalassiosira Fe and light limitation - culture conditions</a><br />
<a href="http://data-mgr.bco-dmo.org/dataset/636775" target="_blank">Thalassiosira Fe and light limitation - NCBI and iMicrobe accessions</a></p>
<p><strong>References:</strong></p>
<p><u>Media:</u><br />
Guillard RRL, Hargraves PE (1993). <em>Stichochrysis immobilis</em> is a diatom, not a chyrsophyte. <em>Phycologia</em> <strong>32:</strong> 234-236.</p>
<p><u>Culturing, RNA Extraction:</u><br />
Chappell, P.D.*, L.P. Whitney*, J.R. Wallace, A.I. Darer, S. Jean-Charles, and B.D. Jenkins. 2015. Genetic indicators of iron limitation in wild populations of <em>Thalassiosira oceanica</em> from the northeast Pacific Ocean – <em>ISME J. </em>9(3): 592-602. doi: 10.1038/ismej.2014.171 (* indicates co-first author)</p>
<p><u>Sequencing:</u><br />
Keeling, P.J. <em>et al.</em> (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. <em>PLoS Biol, 12</em>(6), e1001889. doi: 10.1371/journal.pbio.1001889</p> Methods and Sampling: <p><em>Thalassiosira oceanica</em>&nbsp;<a href="https://ncma.bigelow.org/ccmp1005#.VpkZihgrLcI" target="_blank">(CCMP 1005</a>) and <em>T. weissflogii</em> (<a href="https://ncma.bigelow.org/ccmp1010#.VpkXPBgrKM8" target="_blank">CCMP 1010</a>) isolates were obtained from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (West Boothbay Harbor, ME, USA). <em>T. oceanica was</em>&nbsp;isolated in 1958 at 33.1833°N, 65.25°W North Atlantic; <em>T. weissflogii was&nbsp;</em>isolated in 1969, at approximately 37°N 65°W Gulf Stream, between Bermuda and New York.&nbsp;Culture experiments were performed using a modified version of f/2 made in 0.2 µm filtered and microwave-sterilized Sargasso seawater (Guillard and Hargraves, 1993) see <a href="http://data-mgr.bco-dmo.org/dataset/636567" target="_blank">culture conditions dataset</a>&nbsp;for modifications to f/2 for each different treatment. The inoculum for the low iron treatment came from replete cultures that had undergone two successive dilutions (1:10) into media without added iron, resulting in f/2 media with &lt; 4 nM Fe. All macronutrient stocks were processed through a Chelex® 100 ion-exchange column (Bio-Rad Laboratories Inc., Hercules, CA, USA) containing resin prepared according to Price et al. (1989) and 0.2 µm Acrodisc® filter-sterilized (Pall Corporation, Port Washington, NY, USA). All media preparation and culture transferring was performed in a Class-100 HEPA filtered hood.</p>
<p>For all experiments, triplicate cultures were grown at a light level of 140 E/m<sup>2</sup>/s or 45 E/m<sup>2</sup>/s at 25 <sup>o</sup> C (click on Get Data, above) in a Percival incubator (Percival Scientific, Perry, IA, USA) and incubated gently shaking on a MaxQ® 2000 orbital shaker (Thermo Fisher Scientific, Waltham, MA, USA). Growth of the cultures was monitored daily with fluorescence measurements and cell counts (data not shown). Cultures were harvested when growth of the nutrient limited cultures began to decrease when compared to the replete cultures. Biomass was collected by gentle filtration onto 2 µm filters. Filters were placed in screw cap tubes containing 500 μL Qiagen Buffer RLT (Qiagen, Venlo, Netherlands), flash frozen in liquid nitrogen, and stored at -80<strong>°</strong>C until RNA extractions were conducted.</p>
<p>Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, with the following exceptions:&nbsp; cells were lysed using 0.5 mm and 0.1 mm zirconia/silica beads (BioSpec, Bartlesville, OK, USA) mixed with the lysis buffer and bead beaten until the solution looked homogenous (approximately 1 minute). The lysis solution was then put over Qiashredder columns (Qiagen) to remove any large plant material that could clog the spin columns. To aid in the removal of DNA, two DNase digestions were performed. First, Qiagen’s RNase-free DNase Set (an on-column treatment) was used according to the manufacturer’s instructions. The second DNA removal step was conducted using the Turbo DNA-free kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA was then quantified in duplicate using the Qubit Fluorometer (Life Technologies). Following quantification, RNA samples were pooled and precipitated with a standard ammonium acetate/ethanol precipitation and sent for sequencing.&nbsp;An aliquot of the RNA extracted from individual replicates of the low iron and replete treatments of <em>T. weissflogii</em> (CCMP 1010) were also sent for sequencing.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0962208 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0962208
completed
Bethany D. Jenkins
University of Rhode Island
401-874-7551
Department of Cell and Molecular Biology and Graduate School of Oceanography 279 CBLS, 120 Flagg Road
Kingston
RI
02881
USA
bjenkins@uri.edu
pointOfContact
Phoebe Dreux Chappell
Old Dominion University
757-683-4937
333 Oceanography and Physics Bldg.
Norfolk
VA
23529
USA
pdchappe@odu.edu
pointOfContact
asNeeded
Dataset Version: 2016-01-28
Unknown
species
sample
ENA_sample_accession
ENA_2nd_sample_accession
ENA_expt_accession
ENA_run_accession
ENA_study_accession
ENA_2nd_study_accession
theme
None, User defined
species
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Jenkins_2015
service
Deployment Activity
URI laboratory
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.
Genomic and Transcriptomic Comparison of Iron and Light Physiology in Coastal and Oceanic Diatoms
https://www.bco-dmo.org/project/558170
Genomic and Transcriptomic Comparison of Iron and Light Physiology in Coastal and Oceanic Diatoms
<p><em>Project description from NSF award abstract:</em><br />
Diatoms are among the most important primary producers in the ocean. Coastal species can respond to dynamic inputs of nutrients into the surface ocean and form large biomass blooms. Phytoplankton growth in much of the ocean is limited by one nutrient or another, and species that persist in these environments must be able to function under these low nutrient conditions. Oceanic diatom species have lower Fe requirements for growth and may have evolved to subsist in low Fe environments by changing the composition of Fe-demanding metabolic pathways. Iron and light responsive pathways are intimately linked because of the large Fe requirement of photosynthesis and the potential for both to limit growth and the efficiency of the biological carbon pump. Physiological and field studies have shown that many diatoms are susceptible to Fe/light co-limitation, but we lack information on the biochemical basis for co-limitation and how this differs between diatom species. This project will use a combination of genomics tools to investigate how coastal and oceanic diatoms in the ecologically important <em>Thalassiosira</em> genus respond to differing conditions of Fe and light. The investigators will compare the genome sequence of the oceanic diatom T. oceanica, which has recently been sequenced by the PI in collaboration with Illumina, Inc., to published diatom genomes to identify potential differences and similarities in the Fe and light metabolism in oceanic and coastal diatoms. They will use normalized libraries of Expressed Sequence Tags (EST) to characterize the transcriptome of <em>T. oceanica</em>, an oceanic strain of <em>T. weissflogii</em>, and the coastal diatom <em>T. rotula</em> grown in a matrix of Fe-limiting and replete conditions and at low and growth-saturating light levels. And they will quantify gene expression levels for the transcriptome-wide response in these experiments using digital gene expression (DGE), and use the EST data to map the DGE tags. Data from the DGE and EST experiments will be used to compare how diatom metabolism responds to variable light and Fe concentrations and to identify target genes for following limitation in natural diatom populations. Expression of these genes will be monitored in time-course experiments with additional manipulations of Fe and light levels to identify gene markers indicative of different physiological states using quantitative PCR (qPCR). The investigators will also design antibodies to a select number of proteins to monitor protein expression, and they will use qPCR and antibodies to follow responses in diatom communities in field samples collected from a cruise transitioning between Fe-replete and Fe-limiting environments as part of other funded research efforts. This work will further our understanding of how diatoms are adapted to different environments and what the genetic basis for their ecological success may be. Results from this work will help us predict how diatoms may respond to changing light regimes as a result of increased stratification due to climate change and help predict if species from different habitats will have similar or varied responses.</p>
GeTFeHvCOdia
largerWorkCitation
project
eng; USA
biota
oceans
URI laboratory
2016-01-28
laboratory experiments with temperate diatoms
0
BCO-DMO catalogue of parameters from ENA accessions for transcriptomes of T. oceanica and T. weissflogii grown in varied Fe and light (GeTFeHvCOdia 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/636851.rdf
Name: species
Units: unitless
Description: sample species
http://lod.bco-dmo.org/id/dataset-parameter/636852.rdf
Name: sample
Units: unitless
Description: ENA sample identification: CCMP+isolate_id+conditions
http://lod.bco-dmo.org/id/dataset-parameter/636853.rdf
Name: ENA_sample_accession
Units: unitless
Description: ENA Sample accession number and link
http://lod.bco-dmo.org/id/dataset-parameter/636854.rdf
Name: ENA_2nd_sample_accession
Units: unitless
Description: ENA Secondary Sample accession number and link
http://lod.bco-dmo.org/id/dataset-parameter/636855.rdf
Name: ENA_expt_accession
Units: unitless
Description: ENA Experiment accession number and link
http://lod.bco-dmo.org/id/dataset-parameter/636856.rdf
Name: ENA_run_accession
Units: unitless
Description: ENA Run accession number and link
http://lod.bco-dmo.org/id/dataset-parameter/636857.rdf
Name: ENA_study_accession
Units: unitless
Description: ENA Study accession number and link
http://lod.bco-dmo.org/id/dataset-parameter/636858.rdf
Name: ENA_2nd_study_accession
Units: unitless
Description: ENA Secondary Study accession number and link
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
2170
https://datadocs.bco-dmo.org/file/KAAGoWrf20RNkr/ENA_accessions.csv
ENA_accessions.csv
Primary data file for dataset ID 636831
download
https://www.bco-dmo.org/dataset/636831/data/download
download
onLine
dataset
<p><em>Thalassiosira oceanica</em>&nbsp;<a href="https://ncma.bigelow.org/ccmp1005#.VpkZihgrLcI" target="_blank">(CCMP 1005</a>) and <em>T. weissflogii</em> (<a href="https://ncma.bigelow.org/ccmp1010#.VpkXPBgrKM8" target="_blank">CCMP 1010</a>) isolates were obtained from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (West Boothbay Harbor, ME, USA). <em>T. oceanica was</em>&nbsp;isolated in 1958 at 33.1833°N, 65.25°W North Atlantic; <em>T. weissflogii was&nbsp;</em>isolated in 1969, at approximately 37°N 65°W Gulf Stream, between Bermuda and New York.&nbsp;Culture experiments were performed using a modified version of f/2 made in 0.2 µm filtered and microwave-sterilized Sargasso seawater (Guillard and Hargraves, 1993) see <a href="http://data-mgr.bco-dmo.org/dataset/636567" target="_blank">culture conditions dataset</a>&nbsp;for modifications to f/2 for each different treatment. The inoculum for the low iron treatment came from replete cultures that had undergone two successive dilutions (1:10) into media without added iron, resulting in f/2 media with &lt; 4 nM Fe. All macronutrient stocks were processed through a Chelex® 100 ion-exchange column (Bio-Rad Laboratories Inc., Hercules, CA, USA) containing resin prepared according to Price et al. (1989) and 0.2 µm Acrodisc® filter-sterilized (Pall Corporation, Port Washington, NY, USA). All media preparation and culture transferring was performed in a Class-100 HEPA filtered hood.</p>
<p>For all experiments, triplicate cultures were grown at a light level of 140 E/m<sup>2</sup>/s or 45 E/m<sup>2</sup>/s at 25 <sup>o</sup> C (click on Get Data, above) in a Percival incubator (Percival Scientific, Perry, IA, USA) and incubated gently shaking on a MaxQ® 2000 orbital shaker (Thermo Fisher Scientific, Waltham, MA, USA). Growth of the cultures was monitored daily with fluorescence measurements and cell counts (data not shown). Cultures were harvested when growth of the nutrient limited cultures began to decrease when compared to the replete cultures. Biomass was collected by gentle filtration onto 2 µm filters. Filters were placed in screw cap tubes containing 500 μL Qiagen Buffer RLT (Qiagen, Venlo, Netherlands), flash frozen in liquid nitrogen, and stored at -80<strong>°</strong>C until RNA extractions were conducted.</p>
<p>Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, with the following exceptions:&nbsp; cells were lysed using 0.5 mm and 0.1 mm zirconia/silica beads (BioSpec, Bartlesville, OK, USA) mixed with the lysis buffer and bead beaten until the solution looked homogenous (approximately 1 minute). The lysis solution was then put over Qiashredder columns (Qiagen) to remove any large plant material that could clog the spin columns. To aid in the removal of DNA, two DNase digestions were performed. First, Qiagen’s RNase-free DNase Set (an on-column treatment) was used according to the manufacturer’s instructions. The second DNA removal step was conducted using the Turbo DNA-free kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA was then quantified in duplicate using the Qubit Fluorometer (Life Technologies). Following quantification, RNA samples were pooled and precipitated with a standard ammonium acetate/ethanol precipitation and sent for sequencing.&nbsp;An aliquot of the RNA extracted from individual replicates of the low iron and replete treatments of <em>T. weissflogii</em> (CCMP 1010) were also sent for sequencing.</p>
Specified by the Principal Investigator(s)
<p>Data in SRA and ENA databases is linked as raw sequence data in fastq format.&nbsp;Details of processing of sample files associated with MMETSP sample assemblies on iMicrobe site is given in Keeling <em>et al.</em> 2014</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
PI Supplied Instrument Name: Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Deployment: Jenkins_2015
Jenkins_2015
URI
laboratory
Jenkins_2015
Bethany D. Jenkins
University of Rhode Island
URI
laboratory